---------- Welcome to the OBS population program ---------UmlsAccessTool creation...
UmlsAccessTool OBS_OATOOL_e91_UMLS_umls created.
Ontology <AI/RHEUM, 1993> (AIR) added to the set of ontologies accessed
by OBS_OATOOL_e91_UMLS_umls.
Ontology <DXplain, 1994> (DXP) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Current Dental Terminology (CDT), 2007-2008B> (CDT) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Master Drug Data Base, 2008_08_06> (MDDB) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Read thesaurus, Synthesized Terms, 1999> (RCDSY) added to the
set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Authorized Osteopathic Thesaurus, 2003> (AOT) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Metathesaurus additional entry terms for ICD-9-CM, 2009>
(MTHICD9) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <HCPCS Version of Current Procedural Terminology (CPT), 2008>
(HCPT) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <HL7 Vocabulary Version 2.5, 2003_08_30> (HL7V2.5) added to the
set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Foundational Model of Anatomy Ontology, 2_0> (FMA) added to the
set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Omaha System, 2005> (OMS) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Home Health Care Classification, 2003> (HHC) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Clinical Terms Version 3 (CTV3) (Read Codes), 1999> (RCD) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Standard Product Nomenclature, 2003> (SPN) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Patient Monitoring Guidelines for HIV care and antiretroviral
therapy (ART), 224_2006> (LNC_WHO) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <International Statistical Classification of Diseases and
Related Health Problems, 10th Revision, Australian Modification, January
2000 Release> (ICD10AM) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Alcohol and Other Drug Thesaurus, 2000> (AOD) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Current Procedural Terminology, 2008> (CPT) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Patient Health Questionnaire, 224_1999> (LNC_PHQ_9) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Read thesaurus Americanized Synthesized Terms, 1999> (RCDSA)
added to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Patient Care Data Set, 1997> (PCDS) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <ICD10, American English Equivalents, 1998> (ICD10AE) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Metathesaurus HCPCS Hierarchical Terms, 2008> (MTHHH) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <International Classification for Nursing Practice, 1.0> (ICNP)
added to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Medical Entities Dictionary, 2003> (CPM) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Metathesaurus Version of Minimal Standard Terminology Digestive
Endoscopy, 2001> (MTHMST) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Clinical Classifications Software, 2005> (CCS) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <USP Model Guidelines, 2004> (USPMG) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <COSTAR, 1989-1995> (COSTAR) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Neuronames Brain Hierarchy, 1999> (NEU) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Outcome and Assessment Information Set, 224_2002> (LNC_OASIS)
added to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <HL7 Vocabulary Version 3.0, 2006_05> (HL7V3.0) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Thesaurus of Psychological Index Terms, 2004> (PSY) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <ICPC2 - ICD10 Thesaurus, 7-bit Equivalents, 0412>
(MTHICPC2ICD107B) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Beth Israel Vocabulary, 1.0> (BI) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Diseases Database, 2000> (DDB) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Medical Dictionary for Regulatory Activities Terminology
(MedDRA), 11.0> (MDR) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <HL7 Vocabulary Version 2.5, 7-bit equivalents, 2003_08>
(MTHHL7V2.5) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Healthcare Common Procedure Coding System, 2008> (HCPCS) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Pharmacy Practice Activity Classification, 1998> (PPAC) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <MEDCIN, 3_2008_07_14> (MEDCIN) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Quick Medical Reference (QMR), 1996> (QMR) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Library of Congress Subject Headings, 1990> (LCH) added to the
set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <QMR clinically related terms from Randolph A. Miller, 1999>
(RAM) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <RxNorm Vocabulary, 08AA_080902F> (RXNORM) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Canonical Clinical Problem Statement System, 1999> (CCPSS)
added to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Gold Standard Alchemy, 2008_08_11> (GS) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Metathesaurus FDA Structured Product Labels, 2008_08_26>
(MTHSPL) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Gene Ontology, 2008_04_01> (GO) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <McMaster University Epidemiology Terms, 1992> (MCM) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <SNOMED-2, 2> (SNM) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <ICD-9-CM, 2009> (ICD9CM) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Veterans Health Administration National Drug File, 2008_08_11>
(VANDF) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <SNOMED International, 1998> (SNMI) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Perioperative Nursing Data Set, 2nd edition, 2002> (PNDS) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Minimum Data Set, 2.0, 224_20> (LNC_MDS) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Alternative Billing Concepts, 2008> (ALT) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <DSM-IV, 1994> (DSM4) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <SNOMED Clinical Terms, 2008_07_31> (SNOMEDCT) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <DSM-III-R, 1987> (DSM3R) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <University of Washington Digital Anatomist, 1.7.3> (UWDA) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <NCI Thesaurus, 2008_05D> (NCI) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Online Congenital Multiple Anomaly/Mental Retardation
Syndromes, 1999> (JABL) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <International Classification of Primary Care 2nd Edition,
Electronic, 2E, American English Equivalents, 200203> (MTHICPC2EAE) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Physician Data Query, 2007_02> (PDQ) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Logical Observation Identifier Names and Codes, 224> (LNC)
added to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <ICPC-2 PLUS> (ICPC2P) added to the set of ontologies accessed
by OBS_OATOOL_e91_UMLS_umls.
Ontology <ICPC2 - ICD10 Thesaurus, American English Equivalents, 0412>
(MTHICPC2ICD10AE) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <COSTART, 1995> (CST) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Nursing Interventions Classification (NIC), 2005> (NIC) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <CRISP Thesaurus, 2006> (CSP) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <HUGO Gene Nomenclature, 2008_03> (HUGO) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Nursing Outcomes Classification, 3rd Edition> (NOC) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Multum MediSource Lexicon, 2008_08_01> (MMSL) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Metathesaurus FDA National Drug Code Directory, 2008_08_04>
(MTHFDA) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <UMLS Metathesaurus> (MTH) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <National Drug Data File Plus Source Vocabulary, 2008_08_08>
(NDDF) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <International Classification of Primary Care 2nd Edition,
Electronic, 2E, 200203> (ICPC2EENG) added to the set of ontologies
accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Micromedex DRUGDEX, 2008_08_04> (MMX) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Online Mendelian Inheritance in Man, 2007_12_19> (OMIM) added
to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Metathesaurus Source Terminology Names> (SRC) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <WHO Adverse Reaction Terminology, 1997> (WHO) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <NANDA nursing diagnoses: definitions & classification, 2004>
(NAN) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <MedlinePlus Health Topics, 20080614> (MEDLINEPLUS) added to the
set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <UMDNS: product category thesaurus, 2008> (UMD) added to the set
of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <International Statistical Classification of Diseases and
Related Health Problems, Australian Modification, Americanized English
Equivalents, 2000> (ICD10AMAE) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <The Faces, Legs, Activity, Cry, and Consolability (FLACC)
Scale, 224_1997> (LNC_FLACC) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <The Braden Scale for Predicting Pressure Sore Risk, 224_1988>
(LNC_BRADEN) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <ICD10, 1998> (ICD10) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <International Classification of Primary Care, 1993> (ICPC)
added to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <ICPC2 - ICD10 Thesaurus, 200412> (ICPC2ICD10ENG) added to the
set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <National Drug File - Reference Terminology Public Inferred
Edition, 2008_03_11> (NDFRT) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Medical Subject Headings, 2009_2008_08_06> (MSH) added to the
set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <HCPCS Version of Current Dental Terminology (CDT), 2007-2008B>
(HCDT) added to the set of ontologies accessed by
OBS_OATOOL_e91_UMLS_umls.
Ontology <Metathesaurus CPT Hierarchical Terms, 2008> (MTHCH) added to
the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <UltraSTAR, 1993> (ULT) added to the set of ontologies accessed
by OBS_OATOOL_e91_UMLS_umls.
Ontology <NCBI Taxonomy, 2008_05_07> (NCBI) added to the set of
ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
Ontology <Read thesaurus, American English Equivalents, 1999> (RCDAE)
added to the set of ontologies accessed by OBS_OATOOL_e91_UMLS_umls.
BioPortalAccessTool creation...
BioPortaAccessTool OBS_OATOOL_cd7_BIOPORTAL_bioportal created.
Ontology <Drosophila development> (39019) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Units of measurement> (39649) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Human disease> (39228) added to the set of ontologies accessed
by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Sequence types and features> (39708) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Situation-Based Access Control> (39798) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Mouse pathology> (39587) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <PRotein Ontology (PRO)> (39797) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Epoch Clinical Trial Ontologies> (8056) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Fungal gross anatomy> (39704) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Pathogen transmission> (39223) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Bleeding History Phenotype> (38563) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Ontology of Glucose Metabolism Disorder> (39580) added to the
set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Vaccine Ontology> (39700) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <carol> (38620) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Ontology for disease genetic investigation> (39579) added to
the set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Ontology for Genetic Interval> (39578) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <BioTop> (38828) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Ontology of Geographical Region> (39577) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Human developmental anatomy, timed version> (13356) added to
the set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <FlyBase Controlled Vocabulary> (39366) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Electrocardiography (ECG) Ontology> (39576) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <SNP-Ontology> (39215) added to the set of ontologies accessed
by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cell type> (39004) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Human developmental anatomy, abstract version> (13352) added to
the set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Ontology of Physics for Biology> (39001) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Basic Vertebrate Anatomy> (4531) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cell Cycle Ontology (A. thaliana)> (38550) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Evidence codes> (39628) added to the set of ontologies accessed
by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Mouse adult gross anatomy> (39778) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Amino Acid with Simplified Chinese annotations> (39417) added
to the set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Galen> (4525) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Yeast phenotypes> (39354) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Gene Regulation Ontology> (39624) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Fly taxonomy> (13342) added to the set of ontologies accessed
by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Molecular function> (39831) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cellular component> (39830) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Biological process> (39829) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Amino Acid> (4519) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <C. elegans phenotype> (39769) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Zebrafish anatomy and development> (39496) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Mammalian phenotype> (39824) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Foundational Model of Anatomy> (4513) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Suggested Ontology for Pharmacogenomics> (39343) added to the
set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <human phenotype ontology> (39823) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <NCBI organismal classification> (38802) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Teleost anatomy and development> (39762) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Microarray experimental conditions> (38801) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Mass spectrometry> (39281) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cell Cycle Ontology (S. pombe)> (36430) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Proteomics Pipeline Infrastructure for CPTAC> (39549) added to
the set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <C. elegans development> (25148) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Drosophila gross anatomy> (39608) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Proteomics Pipeline Infrastructure for CPTAC> (39546) added to
the set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cell Cycle Ontology (S. cerevisiae)> (36425) added to the set
of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Protein Ontology> (3905) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <BioPortal Metadata> (39545) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <DermLex: The Dermatology Lexicon> (39815) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Parasite Life Cycle> (39544) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Mouse gross anatomy and development> (13323) added to the set
of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Medaka fish anatomy and development> (3093) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Sequence Ontology> (36782) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Phenotypic quality> (39692) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Mosquito gross anatomy> (39331) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <NCI Thesaurus> (39478) added to the set of ontologies accessed
by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cell Cycle Ontology (H. sapiens)> (36417) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <MaHCO - An MHC Ontology> (39804) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Multiple alignment> (3083) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Pseudogene> (38873) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Dictyostelium discoideum anatomy> (36622) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Amphibian gross anatomy> (37911) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Environment Ontology> (39531) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Ontology for Biomedical Investigations> (39317) added to the
set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Physico-chemical process> (13397) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Xenopus anatomy and development> (39046) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <ICD9> (35686) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <African Traditional Medicine> (32145) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Common Anatomy Reference Ontology> (13305) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Computer-based Patient Record Ontology> (39734) added to the
set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <BIRNLex> (29684) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Biomedical Resource Ontology> (39521) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Plant growth and developmental stage> (37419) added to the set
of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <C. elegans gross anatomy> (39728) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cardiac Electrophysiology Ontology> (39038) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Proteomics data and process provenance> (13386) added to the
set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Pathway ontology> (39665) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <RadLex> (21275) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <NIFSTD> (39664) added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Plant structure> (39724) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Spider Ontology> (38644) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Plant environmental conditions> (39183) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Teleost taxonomy> (39662) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Sample processing and separation techniques> (39509) added to
the set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Protein-protein interaction> (39508) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Chemical entities of biological interest> (39658) added to the
set of ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Ascomycete phenotype ontology> (39718) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cancer Research and Management ACGT Master Ontology> (38787)
added to the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Cereal plant trait> (31197) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Biological imaging methods> (3057) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <NanoParticle Ontology> (39717) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Spatial Ontology> (38996) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Tick gross anatomy> (38366) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Experimental Factor Ontology> (39715) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Rat Strain Ontology> (39234) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Lipid Ontology> (39503) added to the set of ontologies accessed
by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Family Health History Ontology> (38631) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Subcellular Anatomy Ontology (SAO)> (14391) added to the set of
ontologies accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <Infectious disease> (39501) added to the set of ontologies
accessed by OBS_OATOOL_cd7_BIOPORTAL_bioportal.
Ontology <NIFSTD> was not in the set of ontologies accessed by
OBS_OATOOL_cd7_BIOPORTAL_bioportal.
ObsJaxMgdAccessTool creation...
Loading JAXMGD ontology in memory with local file JAX_Mouse_Gene_Dict.txt
...
Ontology <Mouse/Human Gene dictionary> (JAXMGD) added to the set of
ontologies accessed by OBS_OATOOL_10e_JAXMGD_jaxmgd.
ObsJaxMgdAccessTool OBS_OATOOL_10e_JAXMGD_jaxmgd created.
* Populate OntologyTable... Table OBS_OT already contains an entry for
the ontology: AIR.
Table OBS_OT already contains an entry for the ontology: NAN.
Table OBS_OT already contains an entry for the ontology: ICPC2P.
Table OBS_OT already contains an entry for the ontology: ULT.
Table OBS_OT already contains an entry for the ontology: MTHSPL.
Table OBS_OT already contains an entry for the ontology: MMX.
Table OBS_OT already contains an entry for the ontology: HCDT.
Table OBS_OT already contains an entry for the ontology: MSH.
Table OBS_OT already contains an entry for the ontology: CPT.
Table OBS_OT already contains an entry for the ontology: MTHICPC2ICD107B.
Table OBS_OT already contains an entry for the ontology: QMR.
Table OBS_OT already contains an entry for the ontology: CSP.
Table OBS_OT already contains an entry for the ontology: AOT.
Table OBS_OT already contains an entry for the ontology: LNC_MDS.
Table OBS_OT already contains an entry for the ontology: MTHHH.
Table OBS_OT already contains an entry for the ontology: MDDB.
Table OBS_OT already contains an entry for the ontology: SPN.
Table OBS_OT already contains an entry for the ontology: NIC.
Table OBS_OT already contains an entry for the ontology: USPMG.
Table OBS_OT already contains an entry for the ontology: RCDSY.
Table OBS_OT already contains an entry for the ontology: ICPC2EENG.
Table OBS_OT already contains an entry for the ontology: MTHMST.
Table OBS_OT already contains an entry for the ontology: HCPT.
Table OBS_OT already contains an entry for the ontology: PDQ.
Table OBS_OT already contains an entry for the ontology: FMA.
Table OBS_OT already contains an entry for the ontology: GO.
Table OBS_OT already contains an entry for the ontology: PNDS.
Table OBS_OT already contains an entry for the ontology: LCH.
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
MTHHL7V2.5.
LNC_BRADEN.
ICNP.
RAM.
MEDCIN.
LNC_PHQ_9.
SNM.
NEU.
MEDLINEPLUS.
SNMI.
RXNORM.
DSM4.
MTHICPC2EAE.
PSY.
MTHICD9.
ICD9CM.
BI.
AOD.
OMIM.
HL7V3.0.
MTHCH.
DSM3R.
RCDAE.
OMS.
NDDF.
HCPCS.
CST.
HHC.
NOC.
DXP.
ICD10AE.
WHO.
CDT.
ICPC2ICD10ENG.
RCD.
MDR.
MTHICPC2ICD10AE.
COSTAR.
ALT.
MTH.
ICD10AMAE.
JABL.
LNC_WHO.
CPM.
LNC_OASIS.
SRC.
PCDS.
UMD.
RCDSA.
NCI.
GS.
LNC_FLACC.
PPAC.
CCPSS.
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
Table
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
OBS_OT
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
already
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
contains
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
an
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
entry
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
the
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
UWDA.
ICPC.
ICD10.
HL7V2.5.
MMSL.
HUGO.
DDB.
MTHFDA.
SNOMEDCT.
CCS.
NDFRT.
NCBI.
LNC.
VANDF.
MCM.
ICD10AM.
39004.
3093.
3057.
39223.
38366.
39215.
36417.
38996.
39281.
36782.
39234.
4519.
38787.
13305.
38631.
25148.
13323.
32145.
39001.
39019.
13386.
3083.
38873.
37911.
39038.
38828.
39046.
13397.
8056.
4531.
4525.
35686.
13352.
38801.
39228.
36430.
13356.
38644.
Table OBS_OT already contains an entry for the ontology: 3905.
Table OBS_OT already contains an entry for the ontology: 38620.
Table OBS_OT already contains an entry for the ontology: 36425.
Table OBS_OT already contains an entry for the ontology: 37419.
Table OBS_OT already contains an entry for the ontology: 36622.
Table OBS_OT already contains an entry for the ontology: 38550.
Table OBS_OT already contains an entry for the ontology: 39183.
Table OBS_OT already contains an entry for the ontology: 13342.
Table OBS_OT already contains an entry for the ontology: 31197.
Table OBS_OT already contains an entry for the ontology: JAXMGD.
60 ontologies added.
* Populate ConceptTables and directParents/directChildren...
0 concepts added [00h 00m 00s] for ontology: AIR.
0 concepts added [00h 00m 00s] for ontology: NAN.
0 concepts added [00h 00m 00s] for ontology: ICPC2P.
0 concepts added [00h 00m 00s] for ontology: ULT.
0 concepts added [00h 00m 00s] for ontology: MTHSPL.
0 concepts added [00h 00m 00s] for ontology: MMX.
0 concepts added [00h 00m 00s] for ontology: HCDT.
0 concepts added [00h 00m 00s] for ontology: MSH.
0 concepts added [00h 00m 00s] for ontology: CPT.
0 concepts added [00h 00m 00s] for ontology: MTHICPC2ICD107B.
0 concepts added [00h 00m 00s] for ontology: QMR.
0 concepts added [00h 00m 00s] for ontology: CSP.
0 concepts added [00h 00m 00s] for ontology: AOT.
0 concepts added [00h 00m 00s] for ontology: LNC_MDS.
0 concepts added [00h 00m 00s] for ontology: MTHHH.
0 concepts added [00h 00m 00s] for ontology: MDDB.
0 concepts added [00h 00m 00s] for ontology: SPN.
0 concepts added [00h 00m 00s] for ontology: NIC.
0 concepts added [00h 00m 00s] for ontology: USPMG.
0 concepts added [00h 00m 00s] for ontology: RCDSY.
0 concepts added [00h 00m 00s] for ontology: ICPC2EENG.
0 concepts added [00h 00m 00s] for ontology: MTHMST.
0 concepts added [00h 00m 00s] for ontology: HCPT.
0 concepts added [00h 00m 00s] for ontology: PDQ.
0 concepts added [00h 00m 00s] for ontology: FMA.
0 concepts added [00h 00m 00s] for ontology: GO.
0 concepts added [00h 00m 00s] for ontology: PNDS.
0 concepts added [00h 00m 00s] for ontology: LCH.
0 concepts added [00h 00m 00s] for ontology: MTHHL7V2.5.
0 concepts added [00h 00m 00s] for ontology: LNC_BRADEN.
0 concepts added [00h 00m 00s] for ontology: ICNP.
0 concepts added [00h 00m 00s] for ontology: RAM.
0 concepts added [00h 00m 00s] for ontology: MEDCIN.
0 concepts added [00h 00m 00s] for ontology: LNC_PHQ_9.
0 concepts added [00h 00m 00s] for ontology: SNM.
0 concepts added [00h 00m 00s] for ontology: NEU.
0 concepts added [00h 00m 00s] for ontology: MEDLINEPLUS.
0 concepts added [00h 00m 00s] for ontology: SNMI.
0 concepts added [00h 00m 00s] for ontology: RXNORM.
0 concepts added [00h 00m 00s] for ontology: DSM4.
0 concepts added [00h 00m 00s] for ontology: MTHICPC2EAE.
0 concepts added [00h 00m 00s] for ontology: PSY.
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
concepts
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
added
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
[00h
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00m
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
00s]
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
for
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
ontology:
MTHICD9.
ICD9CM.
BI.
AOD.
OMIM.
HL7V3.0.
MTHCH.
DSM3R.
RCDAE.
OMS.
NDDF.
HCPCS.
CST.
HHC.
NOC.
DXP.
ICD10AE.
WHO.
CDT.
ICPC2ICD10ENG.
RCD.
MDR.
MTHICPC2ICD10AE.
COSTAR.
ALT.
MTH.
ICD10AMAE.
JABL.
LNC_WHO.
CPM.
LNC_OASIS.
SRC.
PCDS.
UMD.
RCDSA.
NCI.
GS.
LNC_FLACC.
PPAC.
CCPSS.
UWDA.
ICPC.
ICD10.
HL7V2.5.
MMSL.
HUGO.
DDB.
MTHFDA.
SNOMEDCT.
CCS.
NDFRT.
NCBI.
LNC.
VANDF.
0 concepts added [00h 00m 00s] for ontology: MCM.
0 concepts added [00h 00m 00s] for ontology: ICD10AM.
0 ontologies added.
* Populate ConceptTables and directParents/directChildren with
BioPortal...
Processing ontology: Foundational Model of Anatomy (4513)... 78988
concepts added in [00h 54m 10s] for ontology: 4513.
Processing ontology: Electrocardiography (ECG) Ontology (39576)...
392 concepts added in [00h 00m 13s] for ontology: 39576.
Processing ontology: Mosquito gross anatomy (39331)... 1861
concepts added in [00h 06m 03s] for ontology: 39331.
Processing ontology: C. elegans phenotype (39769)... 1824 concepts
added in [00h 03m 00s] for ontology: 39769.
Processing ontology: Ontology for Biomedical Investigations
(39317)... 1364 concepts added in [00h 00m 47s] for ontology: 39317.
0 concepts added in [00h 00m 00s] for ontology: 39004.
0 concepts added in [00h 00m 00s] for ontology: 3093.
0 concepts added in [00h 00m 00s] for ontology: 3057.
Processing ontology: Evidence codes (39628)... 149 concepts added
in [00h 00m 10s] for ontology: 39628.
Processing ontology: Ontology of Geographical Region (39577)... 39
concepts added in [00h 00m 02s] for ontology: 39577.
0 concepts added in [00h 00m 00s] for ontology: 39223.
Processing ontology: Phenotypic quality (39692)... 1134 concepts
added in [00h 01m 25s] for ontology: 39692.
Processing ontology: BioPortal Metadata (39545)... 95 concepts
added in [00h 00m 04s] for ontology: 39545.
Processing ontology: Teleost taxonomy (39662)... 36596 concepts
added in [01h 05m 18s] for ontology: 39662.
0 concepts added in [00h 00m 00s] for ontology: 38366.
0 concepts added in [00h 00m 00s] for ontology: 39215.
Processing ontology: Mouse adult gross anatomy (39778)... 2882
concepts added in [00h 08m 27s] for ontology: 39778.
Processing ontology: Pathway ontology (39665)... 648 concepts added
in [00h 01m 03s] for ontology: 39665.
0 concepts added in [00h 00m 00s] for ontology: 36417.
0 concepts added in [00h 00m 00s] for ontology: 38996.
Processing ontology: NIFSTD (39664)... 12000 concepts added in [00h
07m 27s] for ontology: 39664.
0 concepts added in [00h 00m 00s] for ontology: 39281.
0 concepts added in [00h 00m 00s] for ontology: 36782.
Processing ontology: Gene Regulation Ontology (39624)... 439
concepts added in [00h 00m 14s] for ontology: 39624.
Processing ontology: Sequence types and features (39708)... 13
concepts added in [00h 00m 02s] for ontology: 39708.
Processing ontology: Chemical entities of biological interest
(39658)... 20274 concepts added in [01h 18m 55s] for ontology: 39658.
Processing ontology: human phenotype ontology (39823)... 8984
concepts added in [00h 12m 16s] for ontology: 39823.
Processing ontology: NCI Thesaurus (39478)...
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry:
[39478/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 39478/Retired_Concepts, 1]
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry: [39478/Autologous-Dendritic-Cells_Candida-Albicans-SkinTest-Reagent_CD40-Ligand_gp100-Antigen_Interferon-Gamma_Interleukin4_MART-1-Antigen_Sargramostim_Tyrosinase-Peptide, 39478/NonCurrent_Chemotherapy_Regimen_or_Association, 1]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry: [39478/Autologous-Dendritic-Cells_Candida-Albicans-SkinTest-Reagent_CD40-Ligand_gp100-Antigen_Interferon-Gamma_Interleukin4_MART-1-Antigen_Sargramostim_Tyrosinase-Peptide, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry:
[39478/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
39478/Adverse_Event_Associated_with_Infection, 1]
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478/Adverse_Event_Associated_with_Infection, 1]
com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for
column 'localConceptID' at row 1
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
39478, false]
com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for
column 'localConceptID' at row 1
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[39478/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 39478, false]
70923 concepts added in [05h 31m 36s] for ontology: 39478.
0 concepts added in [00h 00m 00s] for ontology: 39234.
0 concepts added in [00h 00m 00s] for ontology: 4519.
0 concepts added in [00h 00m 00s] for ontology: 38787.
0 concepts added in [00h 00m 00s] for ontology: 13305.
Processing ontology: DermLex: The Dermatology Lexicon (39815)...
6101 concepts added in [00h 05m 37s] for ontology: 39815.
Processing ontology: Subcellular Anatomy Ontology (SAO) (14391)...
821 concepts added in [00h 00m 47s] for ontology: 14391.
0 concepts added in [00h 00m 00s] for ontology: 38631.
Processing ontology: Sample processing and separation techniques
(39509)... 194 concepts added in [00h 00m 17s] for ontology: 39509.
0 concepts added in [00h 00m 00s] for ontology: 25148.
Processing ontology: Protein-protein interaction (39508)... 906
concepts added in [00h 02m 00s] for ontology: 39508.
Processing ontology: Experimental Factor Ontology (39715)... 1626
concepts added in [00h 01m 15s] for ontology: 39715.
Processing ontology: NanoParticle Ontology (39717)... 919 concepts
added in [00h 01m 19s] for ontology: 39717.
Processing ontology: Fungal gross anatomy (39704)... 70 concepts
added in [00h 00m 08s] for ontology: 39704.
Processing ontology: Ontology for Genetic Interval (39578)... 202
concepts added in [00h 00m 10s] for ontology: 39578.
0 concepts added in [00h 00m 00s] for ontology: 13323.
0 concepts added in [00h 00m 00s] for ontology: 32145.
0 concepts added in [00h 00m 00s] for ontology: 39001.
0 concepts added in [00h 00m 00s] for ontology: 39019.
Processing ontology: Ascomycete phenotype ontology (39718)... 268
concepts added in [00h 00m 37s] for ontology: 39718.
Processing ontology: Ontology for disease genetic investigation
(39579)... 388 concepts added in [00h 00m 17s] for ontology: 39579.
0 concepts added in [00h 00m 00s] for ontology: 13386.
0 concepts added in [00h 00m 00s] for ontology: 3083.
Processing ontology: BIRNLex (29684)... 3580 concepts added in [00h
03m 04s] for ontology: 29684.
0 concepts added in [00h 00m 00s] for ontology: 38873.
Processing ontology: Biomedical Resource Ontology (39521)... 407
concepts added in [00h 00m 28s] for ontology: 39521.
Processing ontology: Bleeding History Phenotype (38563)... 302
concepts added in [00h 00m 13s] for ontology: 38563.
Processing ontology: Teleost anatomy and development (39762)...
2457 concepts added in [00h 07m 09s] for ontology: 39762.
Processing ontology: Environment Ontology (39531)... 1223 concepts
added in [00h 02m 52s] for ontology: 39531.
0 concepts added in [00h 00m 00s] for ontology: 37911.
Processing ontology: Situation-Based Access Control (39798)... 150
concepts added in [00h 00m 09s] for ontology: 39798.
0 concepts added in [00h 00m 00s] for ontology: 39038.
Processing ontology: Suggested Ontology for Pharmacogenomics
(39343)... 8645 concepts added in [00h 41m 01s] for ontology: 39343.
Processing ontology: Vaccine Ontology (39700)... 1633 concepts
added in [00h 01m 22s] for ontology: 39700.
0 concepts added in [00h 00m 00s] for ontology: 38828.
0 concepts added in [00h 00m 00s] for ontology: 39046.
Processing ontology: Ontology of Glucose Metabolism Disorder
(39580)... 182 concepts added in [00h 00m 19s] for ontology: 39580.
0 concepts added in [00h 00m 00s] for ontology: 13397.
Processing ontology: Infectious disease (39501)... 152 concepts
added in [00h 00m 25s] for ontology: 39501.
0 concepts added in [00h 00m 00s] for ontology: 8056.
0 concepts added in [00h 00m 00s] for ontology: 4531.
Processing ontology: Amino Acid with Simplified Chinese annotations
(39417)... 46 concepts added in [00h 00m 03s] for ontology: 39417.
0 concepts added in [00h 00m 00s] for ontology: 4525.
Processing ontology: Computer-based Patient Record Ontology
(39734)... 223 concepts added in [00h 00m 14s] for ontology: 39734.
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39546)... 14 concepts added in [00h 00m 00s] for ontology: 39546.
0 concepts added in [00h 00m 00s] for ontology: 35686.
Processing ontology: Mammalian phenotype (39824)... 6728 concepts
added in [00h 09m 25s] for ontology: 39824.
0 concepts added in [00h 00m 00s] for ontology: 13352.
0 concepts added in [00h 00m 00s] for ontology: 38801.
Processing ontology: Lipid Ontology (39503)... 715 concepts added
in [00h 00m 41s] for ontology: 39503.
Processing ontology: Yeast phenotypes (39354)... 251 concepts added
in [00h 00m 39s] for ontology: 39354.
Processing ontology: Molecular function (39831)... 27205 concepts
added in [01h 53m 24s] for ontology: 39831.
0 concepts added in [00h 00m 00s] for ontology: 39228.
0 concepts added in [00h 00m 00s] for ontology: 36430.
Processing ontology: PRotein Ontology (PRO) (39797)... 1823
concepts added in [00h 05m 07s] for ontology: 39797.
Processing ontology: Drosophila gross anatomy (39608)... 6369
concepts added in [00h 19m 00s] for ontology: 39608.
0 concepts added in [00h 00m 00s] for ontology: 13356.
Processing ontology: MaHCO - An MHC Ontology (39804)... 6720
concepts added in [00h 04m 46s] for ontology: 39804.
Processing ontology: Plant structure (39724)... 809 concepts added
in [00h 02m 24s] for ontology: 39724.
Processing ontology: FlyBase Controlled Vocabulary (39366)... 686
concepts added in [00h 01m 07s] for ontology: 39366.
Processing ontology: Zebrafish anatomy and development (39496)...
2219 concepts added in [00h 13m 55s] for ontology: 39496.
0 concepts added in [00h 00m 00s] for ontology: 38644.
Processing ontology: Units of measurement (39649)... 1392 concepts
added in [00h 01m 58s] for ontology: 39649.
Processing ontology: Mouse pathology (39587)... 588 concepts added
in [00h 01m 20s] for ontology: 39587.
0 concepts added in [00h 00m 00s] for ontology: 3905.
0 concepts added in [00h 00m 00s] for ontology: 38620.
0 concepts added in [00h 00m 00s] for ontology: 36425.
0 concepts added in [00h 00m 00s] for ontology: 37419.
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39549)... 15 concepts added in [00h 00m 01s] for ontology: 39549.
0 concepts added in [00h 00m 00s] for ontology: 36622.
0 concepts added in [00h 00m 00s] for ontology: 38550.
0 concepts added in [00h 00m 00s] for ontology: 39183.
Processing ontology: Parasite Life Cycle (39544)... 41 concepts
added in [00h 00m 01s] for ontology: 39544.
Processing ontology: C. elegans gross anatomy (39728)... 3715
concepts added in [00h 44m 26s] for ontology: 39728.
Processing ontology: NCBI organismal classification (38802)...
ERROR: 'White spaces are required between publicId and systemId.'
ERROR: 'com.sun.org.apache.xml.internal.utils.WrappedRuntimeException:
White spaces are required between publicId and systemId.'
2009-04-22 03:33:11,734 ERROR [obs.ontologyAccess.util.XmlUtils] - Error
- Could not transform XML source with XSLT
file:javax.xml.transform.stream.StreamSource@7d868e4f
** PROBLEM: Cannot get concept bean from BioPortal for localConceptID:
38802/NCBITaxon:357819. Null returned.
** Concept 38802/NCBITaxon:357819has a problem.
** PROBLEM: Cannot get concept bean from BioPortal for localConceptID:
38802/NCBITaxon:248365. Null returned.
** Concept 38802/NCBITaxon:248365has a problem.
** PROBLEM: Cannot get concept bean from BioPortal for localConceptID:
38802/NCBITaxon:438168. Null returned.
** Concept 38802/NCBITaxon:438168has a problem.
455536 concepts added in [49h 24m 59s] for ontology: 38802.
0 concepts added in [00h 00m 00s] for ontology: 13342.
Processing ontology: RadLex (21275)... 2009-04-23 09:54:30,256 WARN
[org.apache.commons.httpclient.HttpMethodBase] - Going to buffer response
body of large or unknown size. Using getResponseBodyAsStream instead is
recommended.
11593 concepts added in [00h 09m 57s] for ontology: 21275.
0 concepts added in [00h 00m 00s] for ontology: 31197.
Processing ontology: Biological process (39829)... 27205 concepts
added in [02h 18m 17s] for ontology: 39829.
60 ontolgies added.
0 concepts added [00h 00m 00s] for ontology: JAXMGD.
0 ontologies added.
849926 total concepts added in [68h 34m 45s].
* Populate HierarchyTables...
Processing ontology: Electrocardiography (ECG) Ontology (39576)...
Dumping all the concepts... (392)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 09s].
Processing ontology: Foundational Model of Anatomy (4513)...
Dumping all the concepts... (78988)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [02h 19m 08s].
Processing ontology: C. elegans phenotype (39769)...
Dumping all the concepts... (1824)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 02m 05s].
Processing ontology: Ontology of Geographical Region (39577)...
Dumping all the concepts... (39)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: Phenotypic quality (39692)...
Dumping all the concepts... (1134)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 52s].
Processing ontology: BioPortal Metadata (39545)...
Dumping all the concepts... (95)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 02s].
Processing ontology: Teleost taxonomy (39662)...
Dumping all the concepts... (36596)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [01h 18m 59s].
Processing ontology: Pathway ontology (39665)...
Dumping all the concepts... (648)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 28s].
Processing ontology: NIFSTD (39664)...
Dumping all the concepts... (12000)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
,28,29,30,31,32,33,34,35,36,37,38,39,40,41,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 18m 21s].
Processing ontology: Sequence types and features (39708)...
Dumping all the concepts... (13)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: human phenotype ontology (39823)...
Dumping all the concepts... (8984)
Step 1 - Computing the direct children and filling the
tables...
-------------------------------------------- STOP HERE MANUALLY TO
RESTART DB2 SERVER ---------------------------------------Removing ontology 39823 and dependencies from the OBS DB...
Ontology 39823 and dependencies removed from the OBS DB.
* Populate OntologyTable... 0 ontologies added.
* Populate ConceptTables and directParents/directChildren...
0 ontologies added.
* Populate ConceptTables and directParents/directChildren with
BioPortal...
0 ontolgies added.
0 total concepts added in [00h 00m 00s].
* Populate HierarchyTables...
Processing ontology: Ontology for Genetic Interval (39578)...
Dumping all the concepts... (202)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 21s].
Processing ontology: Fungal gross anatomy (39704)...
Dumping all the concepts... (70)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 05s].
Processing ontology: BIRNLex (29684)...
Dumping all the concepts... (3580)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
,28,29,30,31,32,33,34,35,36,37,38,39,40,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 08m 14s].
Processing ontology: Environment Ontology (39531)...
Dumping all the concepts... (1223)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 01m 11s].
Processing ontology: Vaccine Ontology (39700)...
Dumping all the concepts... (1633)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
,28,29,30,31,32,33,34,35,36,37,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 02m 42s].
Processing ontology: Ontology of Glucose Metabolism Disorder
(39580)...
Dumping all the concepts... (182)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 17s].
Processing ontology: Computer-based Patient Record Ontology
(39734)...
Dumping all the concepts... (223)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 15s].
Processing ontology: Mammalian phenotype (39824)...
Dumping all the concepts... (6728)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,
-------------------------------------- RESTARTED AFTER DB2 FAILURE -------------------------------------
Ontology <human phenotype ontology> (39823) added to the set of
ontologies accessed by OBS_OATOOL_1cf_BIOPORTAL_bp.
Ontology <Mammalian phenotype> (39824) added to the set of ontologies
accessed by OBS_OATOOL_1cf_BIOPORTAL_bp.
Removing ontology 39823 and dependencies from the OBS DB...
Ontology 39823 and dependencies removed from the OBS DB.
Removing ontology 39824 and dependencies from the OBS DB...
Ontology 39824 and dependencies removed from the OBS DB.
* Populate OntologyTable... 2 ontologies added.
* Populate ConceptTables and directParents/directChildren...
0 ontologies added.
* Populate ConceptTables and directParents/directChildren with
BioPortal...
Processing ontology: human phenotype ontology (39823)... 8984
concepts added in [00h 17m 02s] for ontology: 39823.
Processing ontology: Mammalian phenotype (39824)... 6728 concepts
added in [00h 12m 27s] for ontology: 39824.
2 ontolgies added.
15712 total concepts added in [00h 29m 29s].
* Populate HierarchyTables...
Processing ontology: human phenotype ontology (39823)...
Dumping all the concepts... (8984)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [04h 27m 57s].
Processing ontology: Mammalian phenotype (39824)...
Dumping all the concepts... (6728)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [06h 01m 20s].
Processing ontology: Yeast phenotypes (39354)...
Dumping all the concepts... (251)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
--------------- MANUALLY STOPPED BECAUSE OF DB2 PROBLEMS (INDEXES
BROKEN?) ------------------------Removing ontology 39190 and dependencies from the OBS DB...
Ontology 39190 and dependencies removed from the OBS DB.
Removing ontology 39191 and dependencies from the OBS DB...
Ontology 39191 and dependencies removed from the OBS DB.
* Populate OntologyTable... 0 ontologies added.
* Populate ConceptTables and directParents/directChildren...
0 ontologies added.
* Populate ConceptTables and directParents/directChildren with
BioPortal...
0 ontolgies added.
0 total concepts added in [00h 00m 00s].
* Populate HierarchyTables...
Processing ontology: Yeast phenotypes (39354)...
Dumping all the concepts... (251)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 05s].
Processing ontology: MaHCO - An MHC Ontology (39804)...
Dumping all the concepts... (6720)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 14m 47s].
Processing ontology: FlyBase Controlled Vocabulary (39366)...
Dumping all the concepts... (686)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 23s].
Processing ontology: Parasite Life Cycle (39544)...
Dumping all the concepts... (41)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: RadLex (21275)...
Dumping all the concepts... (11593)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 08m 14s].
Processing ontology: Mosquito gross anatomy (39331)...
Dumping all the concepts... (1861)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 03m 38s].
Processing ontology: Ontology for Biomedical Investigations
(39317)...
Dumping all the concepts... (1364)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 01m 09s].
Processing ontology: Evidence codes (39628)...
Dumping all the concepts... (149)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 04s].
Processing ontology: Mouse adult gross anatomy (39778)...
Dumping all the concepts... (2882)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 06m 39s].
Processing ontology: Gene Regulation Ontology (39624)...
Dumping all the concepts... (439)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 17s].
Processing ontology: Chemical entities of biological interest
(39658)...
Dumping all the concepts... (20274)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 51m 27s].
Processing ontology: NCI Thesaurus (39478)...
Dumping all the concepts... (70923)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 25m 56s].
Processing ontology: DermLex: The Dermatology Lexicon (39815)...
Dumping all the concepts... (6101)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 04m 32s].
Processing ontology: Subcellular Anatomy Ontology (SAO) (14391)...
Dumping all the concepts... (821)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 31s].
Processing ontology: Sample processing and separation techniques
(39509)...
Dumping all the concepts... (194)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 06s].
Processing ontology: Protein-protein interaction (39508)...
Dumping all the concepts... (906)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 27s].
Processing ontology: Experimental Factor Ontology (39715)...
Dumping all the concepts... (1626)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 57s].
Processing ontology: NanoParticle Ontology (39717)...
Dumping all the concepts... (919)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 01m 24s].
Processing ontology: Ascomycete phenotype ontology (39718)...
Dumping all the concepts... (268)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 05s].
Processing ontology: Ontology for disease genetic investigation
(39579)...
Dumping all the concepts... (388)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 14s].
Processing ontology: Biomedical Resource Ontology (39521)...
Dumping all the concepts... (407)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 00m 10s].
Processing ontology: Bleeding History Phenotype (38563)...
Dumping all the concepts... (302)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
com.mysql.jdbc.exceptions.MySQLSyntaxErrorException: You have an error in
your SQL syntax; check the manual that corresponds to your MySQL server
version for the right syntax to use near 's Syndrome Assesment Form',
'38563/Shift in Body Fat Distribution', '38563/Banda' at line 1
** PROBLEM ** Cannot get entries on table OBS_PTLT with leaf concepts:
[38563/Umbilical Cord Separation, 38563/CNS Bleeding Event Form,
38563/Bloody Stool, 38563/von Willebrand Factor concentrate, 38563/Factor
IX Deficiency, 38563/Bruising History Form, 38563/Cryopercipitate,
38563/Sigmoidoscopy, 38563/Bacterial Infection, 38563/Texture of Stool,
38563/Desmopressin Injection, 38563/:PAL-CONSTRAINT, 38563/Factor XIII
concentrate, 38563/Colonoscopy, 38563/Inhalation Anesthesia, 38563/Severe
Minor Wound Bleeding Form (V), 38563/Opthalmic Bleeding Event Form,
38563/Teething, 38563/Radiation Therapy, 38563/Kidney Stone Removal,
38563/Left Nostril, 38563/REFERENCE-CLASS, 38563/Loacal Pressure,
38563/Chest, 38563/Menstrual Period, 38563/:DIRECTED-BINARY-RELATION,
38563/Farm injury, 38563/Shaving Cut, 38563/Uterine Ablation,
38563/Bleeding After Tooth Extraction, 38563/Horseback injury,
38563/Cerebral Aneurism, 38563/Ice, 38563/Bleeding From Tongue Form,
38563/Topical Thrombin, 38563/Aspirin Form, 38563/Factor XI concentrate,
38563/Tooth Extraction Form, 38563/Unusual Stool Color Form,
38563/Connective Tissue Assesment Form, 38563/Orbital Bleeding,
38563/NSAID, 38563/Factor VIII Deficiency, 38563/Abnormalities of
Capillaries Form, 38563/Cushing's Syndrome Assesment Form, 38563/Shift in
Body Fat Distribution, 38563/Bandage, 38563/Plasma Transfusion,
38563/Delayed Bleeding From Procedure or Surgery, 38563/Slow Skin
Healing, 38563/Motor vehicle accident injury, 38563/Bronchitis,
38563/:STANDARD-SLOT-CN, 38563/Petechiae, 38563/Umbilical Cord Separation
Form, 38563/Hematoma, 38563/Muscle, 38563/CT Scan, 38563/Relative,
38563/Knee, 38563/Tooth Extraction, 38563/Hematemesis, 38563/Nasal
Packing, 38563/Shaving Cut Form, 38563/Severe Custenous Symptom Form (V),
38563/Hemoptysis, 38563/Hemorrhage From Trauma, 38563/Localized Bruising
Form, 38563/Gastritis, 38563/MIscarriage, 38563/Fat Deposition on Neck,
38563/Avitene Packing, 38563/AMICAR, 38563/Bronchiectasis,
38563/Postnatal Hemorrhage Form, 38563/Face, 38563/Pregnancy Form,
38563/Fragile Scars, 38563/Factor IX concentrate, 38563/Bleeding From
Lips Form, 38563/Menstruation, 38563/Gingival Hemorrhage, 38563/Induced
Delivery, 38563/Hematuria Form, 38563/General Hemarthroses Form,
38563/Other Minor Cut, 38563/Procedure or Surgery Hemorrhage Form,
38563/Cautery, 38563/Uterine Polyp, 38563/Other Surgery,
38563/Bronchoscopy, 38563/Severe Kidney Disease, 38563/Bullet wound,
38563/Bleeding From Lips, 38563/Per Day, 38563/Factor X Deficiency,
38563/Menstruation History Form, 38563/Angiodysplasia, 38563/Cerebral
Hemorrhage, 38563/Dental Regional Nerve Block, 38563/Age, 38563/Angiomas
Form, 38563/Abdomen Stretch Marks, 38563/Factor VII Deficiency,
38563/:STANDARD-FACET, 38563/Factor VIII, 38563/Gingival Hemorrhage Other
Than with Brushing and Flossing Form, 38563/Gauze Packing,
38563/Unmbilical Cord Stump, 38563/Prenatal, 38563/Sports injury,
38563/Caesarian Section, 38563/:INSTANCE-ANNOTATION, 38563/MRI,
38563/Other Minor Cut Form, 38563/Fibring Glue, 38563/Severe Liver
Disease, 38563/Molar, 38563/Hematoma Form, 38563/Intravenous Anesthesia,
38563/Viral Infection, 38563/Antibiotics, 38563/Wrist, 38563/NOREFSYSCLASS, 38563/Epistaxis Form, 38563/Prothrombin Complex Concentrate,
38563/Tuberculosis, 38563/Dilatation and Curettage, 38563/Frenulum,
38563/General Gingival Hemorrhage Form, 38563/Abortion, 38563/Stomach,
38563/Knife wound, 38563/Stroke, 38563/Right Nostril, 38563/FORM-CLASS,
38563/Gingival Hemorrhage With Brushing And Flossing Form, 38563/Patient,
38563/Upper Arm, 38563/Delivery Hemorrhage Form, 38563/Aniodysplasia
Form, 38563/Hematemesis Form, 38563/Unsusual Stool Texture Form,
38563/Heavy Flow During Menstruation Form, 38563/Factor XI Deficiency,
38563/Angioma, 38563/Glass wound, 38563/Telangiectasias Form,
38563/Platelet transfusion, 38563/Elbow, 38563/Gastric Ulcer,
38563/Epistaxis, 38563/Venipuncture Form, 38563/Cytoscopy, 38563/Unusual
Skin Texture, 38563/Esophageal Tear, 38563/NSAID Form, 38563/Tooth Loss,
38563/Abnormal Connective Tissue, 38563/Resurgery, 38563/Duration Range,
38563/Venipuncture, 38563/Localized Hemarthroses Form, 38563/Platelet
Abnormality, 38563/Spider Telangiectasias, 38563/Dental Local By
Injection Anesthesia, 38563/Iron Injections, 38563/Recent Bruising Form,
38563/Postnatal, 38563/Cushing's Syndrome, 38563/Back, 38563/Lower Arm,
38563/Factor V Deficiency, 38563/Linear lace-like red marks,
38563/Permanent, 38563/Loose Skin, 38563/Sutures, 38563/von Willebrand
Factor Deficiency, 38563/Paper Cut, 38563/Physician, 38563/Incisor,
38563/Ultrasound, 38563/Other Thrombocytopenia, 38563/Bleeding From
Tongue, 38563/Uterine Fibroids, 38563/Iron Pills, 38563/Circumcision
Form, 38563/Deciduous, 38563/Hematuria, 38563/Duodenal Ulcer,
38563/Hemoptysis Form, 38563/Teething Form, 38563/Severe Epistaxis From
(V), 38563/Double Jointedness, 38563/Rounded Face, 38563/Canine,
38563/Duration, 38563/Immune Thrombocytopenia, 38563/Bruising Event,
38563/Lips, 38563/Neck, 38563/Factor XIII Deficiency, 38563/Natural or
Developmental Event, 38563/Bruising History, 38563/Hemorrhage During
Pregnancy, 38563/Tranexamic Acid, 38563/Linear Lace-like Red Marks Form,
38563/Scratch, 38563/Other Excessive Hemorrhage, 38563/Trunk, 38563/Oral
Surgery, 38563/Hemathroses, 38563/Esophageal Varices, 38563/Emphysema,
38563/Family Bleeding History Form, 38563/Per Year, 38563/Factor VIIa,
38563/Desmopressin Nasal Spray, 38563/Lower Leg, 38563/Trauma Event Form,
38563/Hysterectomy, 38563/Ankle, 38563/Red Blood Cell Transfusion,
38563/Circumcision, 38563/Thigh]
Ontology hierarchy processed in [00h 00m 03s].
Processing ontology: Teleost anatomy and development (39762)...
Dumping all the concepts... (2457)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 16m 48s].
Processing ontology: Situation-Based Access Control (39798)...
Dumping all the concepts... (150)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 02s].
Processing ontology: Suggested Ontology for Pharmacogenomics
(39343)...
Dumping all the concepts... (8645)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 12m 17s].
Processing ontology: Infectious disease (39501)...
Dumping all the concepts... (152)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 01s].
Processing ontology: Amino Acid with Simplified Chinese annotations
(39417)...
Dumping all the concepts... (46)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39546)...
Dumping all the concepts... (14)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: Cellular component (39830)...
Dumping all the concepts... (27202)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 49m 53s].
Processing ontology: Lipid Ontology (39503)...
Dumping all the concepts... (715)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 47s].
Processing ontology: Molecular function (39831)...
Dumping all the concepts... (27205)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 35m 52s].
Processing ontology: Drosophila gross anatomy (39608)...
Dumping all the concepts... (6369)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,
Step 3 - Completing PTRs on table OBS_PTRT... ...
Step 3bis - Completing PTLs on table OBS_PTLT... ...
Ontology hierarchy processed in [05h 10m 20s].
Processing ontology: PRotein Ontology (PRO) (39797)...
Dumping all the concepts... (1823)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 35s].
Processing ontology: Plant structure (39724)...
Dumping all the concepts... (809)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 03m 29s].
Processing ontology: Zebrafish anatomy and development (39496)...
Dumping all the concepts... (2219)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,
Step 3 - Completing PTRs on table OBS_PTRT... ...
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 16m 48s].
Processing ontology: Units of measurement (39649)...
Dumping all the concepts... (1392)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 01m 02s].
Processing ontology: Mouse pathology (39587)...
Dumping all the concepts... (588)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 22s].
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39549)...
Dumping all the concepts... (15)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: C. elegans gross anatomy (39728)...
Dumping all the concepts... (3715)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 06m 57s].
Processing ontology: NCBI organismal classification (38802)...
Dumping all the concepts... (455536)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
------------------------- RESUME AFTER RONG KILLING OF DEV2 ------------------------------------------------------------Processing ontology: NCBI organismal classification (38802)...
Dumping all the concepts... (455536)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
,28,29,30,31,32,33,34,35,36,37,38,39,40,41,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [21h 46m 12s].
Processing ontology: Biological process (39829)...
Dumping all the concepts... (27205)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
Step 3 - Completing PTRs on table OBS_PTRT... ...
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 34m 53s].
-------------------------- MANUALLY RESTARTED AFTER CODE SYNCHRONISATION
--------------------------------------21 ontologies added.
*** Populate concept tables (OBS_TT & OBS_CT) and
directParents/directChildren (OBS_ISAPT) with BioPortal...
Processing ontology: C. elegans phenotype (39854)... 1829 concepts
added in [00h 03m 10s] for ontology: 39854.
0 concepts added in [00h 00m 00s] for ontology: 4513.
Processing ontology: Electrocardiography (ECG) Ontology (39893)...
497 concepts added in [00h 00m 13s] for ontology: 39893.
0 concepts added in [00h 00m 00s] for ontology: 39331.
0 concepts added in [00h 00m 00s] for ontology: 39317.
Processing ontology: Teleost anatomy and development (39892)...
2477 concepts added in [00h 06m 50s] for ontology: 39892.
0 concepts added in [00h 00m 00s] for ontology: 39004.
0 concepts added in [00h 00m 00s] for ontology: 3093.
0 concepts added in [00h 00m 00s] for ontology: 39628.
0 concepts added in [00h 00m 00s] for ontology: 3057.
Processing ontology: PRotein Ontology (PRO) (39891)... 1823
concepts added in [00h 05m 11s] for ontology: 39891.
0 concepts added in [00h 00m 00s] for ontology: 39577.
0 concepts added in [00h 00m 00s] for ontology: 39223.
Processing ontology: Yeast phenotypes (39909)... 259 concepts added
in [00h 00m 33s] for ontology: 39909.
0 concepts added in [00h 00m 00s] for ontology: 39545.
0 concepts added in [00h 00m 00s] for ontology: 38366.
0 concepts added in [00h 00m 00s] for ontology: 39215.
0 concepts added in [00h 00m 00s] for ontology: 39778.
0 concepts added in [00h 00m 00s] for ontology: 39665.
0 concepts added in [00h 00m 00s] for ontology: 36417.
0 concepts added in [00h 00m 00s] for ontology: 38996.
0 concepts added in [00h 00m 00s] for ontology: 39664.
0 concepts added in [00h 00m 00s] for ontology: 39281.
0 concepts added in [00h 00m 00s] for ontology: 36782.
0 concepts added in [00h 00m 00s] for ontology: 39624.
0 concepts added in [00h 00m 00s] for ontology: 39478.
Processing ontology: Mammalian phenotype (39859)... 6741 concepts
added in [00h 08m 14s] for ontology: 39859.
0 concepts added in [00h 00m 00s] for ontology: 38787.
0 concepts added in [00h 00m 00s] for ontology: 39234.
0 concepts added in [00h 00m 00s] for ontology: 4519.
0 concepts added in [00h 00m 00s] for ontology: 13305.
0 concepts added in [00h 00m 00s] for ontology: 39815.
Processing ontology: Environment Ontology (39858)... 1231 concepts
added in [00h 04m 28s] for ontology: 39858.
0 concepts added in [00h 00m 00s] for ontology: 14391.
0 concepts added in [00h 00m 00s] for ontology: 38631.
Processing ontology: Mosquito insecticide resistance (39915)...
4309 concepts added in [00h 15m 28s] for ontology: 39915.
Processing ontology: Human disease (39857)... 12311 concepts added
in [00h 21m 06s] for ontology: 39857.
0 concepts added in [00h 00m 00s] for ontology: 39509.
0 concepts added in [00h 00m 00s] for ontology: 25148.
Processing ontology: Ascomycete phenotype ontology (39907)... 278
concepts added in [00h 00m 36s] for ontology: 39907.
0 concepts added in [00h 00m 00s] for ontology: 39508.
0 concepts added in [00h 00m 00s] for ontology: 39578.
0 concepts added in [00h 00m 00s] for ontology: 32145.
0 concepts added in [00h 00m 00s] for ontology: 13323.
0 concepts added in [00h 00m 00s] for ontology: 39717.
0 concepts added in [00h 00m 00s] for ontology: 39704.
0 concepts added in [00h 00m 00s] for ontology: 39001.
0 concepts added in [00h 00m 00s] for ontology: 39019.
0 concepts added in [00h 00m 00s] for ontology: 39579.
0 concepts added in [00h 00m 00s] for ontology: 13386.
0 concepts added in [00h 00m 00s] for ontology: 3083.
0 concepts added in [00h 00m 00s] for ontology: 29684.
Processing ontology: Teleost taxonomy (39905)... 36596 concepts
added in [01h 00m 12s] for ontology: 39905.
0 concepts added in [00h 00m 00s] for ontology: 38873.
0 concepts added in [00h 00m 00s] for ontology: 39521.
Processing ontology: Bleeding History Phenotype (38563)... 302
concepts added in [00h 00m 12s] for ontology: 38563.
Processing ontology: Experimental Factor Ontology (39885)... 1640
concepts added in [00h 01m 05s] for ontology: 39885.
0 concepts added in [00h 00m 00s] for ontology: 37911.
0 concepts added in [00h 00m 00s] for ontology: 39798.
0 concepts added in [00h 00m 00s] for ontology: 39038.
0 concepts added in [00h 00m 00s] for ontology: 39343.
0 concepts added in [00h 00m 00s] for ontology: 39700.
Processing ontology: Gene Ontology (39913)... 27342 concepts added
in [02h 12m 33s] for ontology: 39913.
0 concepts added in [00h 00m 00s] for ontology: 38828.
0 concepts added in [00h 00m 00s] for ontology: 39046.
0 concepts added in [00h 00m 00s] for ontology: 39580.
0 concepts added in [00h 00m 00s] for ontology: 13397.
0 concepts added in [00h 00m 00s] for ontology: 39501.
0 concepts added in [00h 00m 00s] for ontology: 8056.
Processing ontology: Computer-based Patient Record Ontology
(39900)... 139 concepts added in [00h 00m 04s] for ontology: 39900.
0 concepts added in [00h 00m 00s] for ontology: 4531.
0 concepts added in [00h 00m 00s] for ontology: 39417.
0 concepts added in [00h 00m 00s] for ontology: 4525.
0 concepts added in [00h 00m 00s] for ontology: 39546.
0 concepts added in [00h 00m 00s] for ontology: 35686.
Processing ontology: human phenotype ontology (39914)... 8972
concepts added in [00h 11m 06s] for ontology: 39914.
0 concepts added in [00h 00m 00s] for ontology: 13352.
0 concepts added in [00h 00m 00s] for ontology: 38801.
Processing ontology: Comparative Data Analysis Ontology (39879)...
125 concepts added in [00h 00m 12s] for ontology: 39879.
0 concepts added in [00h 00m 00s] for ontology: 36430.
0 concepts added in [00h 00m 00s] for ontology: 39608.
0 concepts added in [00h 00m 00s] for ontology: 13356.
0 concepts added in [00h 00m 00s] for ontology: 39804.
0 concepts added in [00h 00m 00s] for ontology: 39724.
0 concepts added in [00h 00m 00s] for ontology: 39366.
Processing ontology: Sequence types and features (39847)... 13
concepts added in [00h 00m 02s] for ontology: 39847.
0 concepts added in [00h 00m 00s] for ontology: 39496.
0 concepts added in [00h 00m 00s] for ontology: 38644.
0 concepts added in [00h 00m 00s] for ontology: 39649.
0 concepts added in [00h 00m 00s] for ontology: 39587.
0 concepts added in [00h 00m 00s] for ontology: 3905.
0 concepts added in [00h 00m 00s] for ontology: 36425.
0 concepts added in [00h 00m 00s] for ontology: 37419.
0 concepts added in [00h 00m 00s] for ontology: 39549.
0 concepts added in [00h 00m 00s] for ontology: 36622.
0 concepts added in [00h 00m 00s] for ontology: 38550.
0 concepts added in [00h 00m 00s] for ontology: 39183.
0 concepts added in [00h 00m 00s] for ontology: 39544.
Processing ontology: Phenotypic quality (39886)... 1134 concepts
added in [00h 01m 22s] for ontology: 39886.
0 concepts added in [00h 00m 00s] for ontology: 38802.
Processing ontology: Chemical entities of biological interest
(39895)... 20403 concepts added in [01h 11m 01s] for ontology: 39895.
Processing ontology: C. elegans gross anatomy (39853)... 3715
concepts added in [00h 41m 53s] for ontology: 39853.
0 concepts added in [00h 00m 00s] for ontology: 13342.
0 concepts added in [00h 00m 00s] for ontology: 21275.
0 concepts added in [00h 00m 00s] for ontology: 31197.
21 ontolgies added.
0 concepts added [00h 00m 00s] for ontology: JAXMGD.
0 ontologies added.
132136 total concepts added in [06h 25m 39s].
*** Populate hierarchy tables (OBS_ISAPT, OBS_PTRT, OBS_PTLT) for UMLS
only...
Hierarchy tables (UMLS) populated in [00h 00m 00s].
*** Populate hierarchy tables (OBS_ISAPT, OBS_PTRT, OBS_PTLT, et Lcui
tables)...
Processing ontology: C. elegans phenotype (39854)...
Dumping all the concepts... (1829)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 01m 55s].
Processing ontology: Foundational Model of Anatomy (4513)...
Dumping all the concepts... (78988)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [02h 05m 57s].
Processing ontology: Electrocardiography (ECG) Ontology (39893)...
Dumping all the concepts... (497)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 09s].
Processing ontology: Mosquito gross anatomy (39331)...
Dumping all the concepts... (1861)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 03m 22s].
Processing ontology: Ontology for Biomedical Investigations
(39317)...
Dumping all the concepts... (1364)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 01m 04s].
Processing ontology: Teleost anatomy and development (39892)...
Dumping all the concepts... (2477)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 17m 08s].
Processing ontology: Evidence codes (39628)...
Dumping all the concepts... (149)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 04s].
Processing ontology: PRotein Ontology (PRO) (39891)...
Dumping all the concepts... (1823)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 28s].
Processing ontology: Ontology of Geographical Region (39577)...
Dumping all the concepts... (39)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: Yeast phenotypes (39909)...
Dumping all the concepts... (259)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 05s].
Processing ontology: BioPortal Metadata (39545)...
Dumping all the concepts... (95)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 01s].
Processing ontology: Mouse adult gross anatomy (39778)...
Dumping all the concepts... (2882)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 06m 31s].
Processing ontology: Pathway ontology (39665)...
Dumping all the concepts... (648)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 21s].
Processing ontology: NIFSTD (39664)...
Dumping all the concepts... (12000)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
,28,29,30,31,32,33,34,35,36,37,38,39,40,41,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 14m 35s].
Processing ontology: Gene Regulation Ontology (39624)...
Dumping all the concepts... (439)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 17s].
Processing ontology: NCI Thesaurus (39478)...
Dumping all the concepts... (70923)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 29m 44s].
Processing ontology: Mammalian phenotype (39859)...
Dumping all the concepts... (6741)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 08m 11s].
Processing ontology: DermLex: The Dermatology Lexicon (39815)...
Dumping all the concepts... (6101)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 04m 14s].
Processing ontology: Environment Ontology (39858)...
Dumping all the concepts... (1231)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 45s].
Processing ontology: Subcellular Anatomy Ontology (SAO) (14391)...
Dumping all the concepts... (821)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 28s].
Processing ontology: Mosquito insecticide resistance (39915)...
Dumping all the concepts... (4309)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 03m 29s].
Processing ontology: Human disease (39857)...
Dumping all the concepts... (12311)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 08m 51s].
Processing ontology: Sample processing and separation techniques
(39509)...
Dumping all the concepts... (194)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 06s].
Processing ontology: Ascomycete phenotype ontology (39907)...
Dumping all the concepts... (278)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 06s].
Processing ontology: Protein-protein interaction (39508)...
Dumping all the concepts... (906)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 23s].
Processing ontology: Ontology for Genetic Interval (39578)...
Dumping all the concepts... (202)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 08s].
Processing ontology: NanoParticle Ontology (39717)...
Dumping all the concepts... (919)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 01m 22s].
Processing ontology: Fungal gross anatomy (39704)...
Dumping all the concepts... (70)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 02s].
Processing ontology: Ontology for disease genetic investigation
(39579)...
Dumping all the concepts... (388)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 13s].
Processing ontology: BIRNLex (29684)...
Dumping all the concepts... (3580)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
,28,29,30,31,32,33,34,35,36,37,38,39,40,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 05m 08s].
Processing ontology: Teleost taxonomy (39905)...
Dumping all the concepts... (36596)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [01h 17m 42s].
Processing ontology: Biomedical Resource Ontology (39521)...
Dumping all the concepts... (407)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 10s].
Processing ontology: Bleeding History Phenotype (38563)...
Dumping all the concepts... (302)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT... ** PROBLEM
** Cannot get entries on table OBS_PTLT with leaf concepts:
[38563/Umbilical Cord Separation, 38563/Bloody Stool, 38563/CNS Bleeding
Event Form, 38563/von Willebrand Factor concentrate, 38563/Factor IX
Deficiency, 38563/Bruising History Form, 38563/Cryopercipitate,
38563/Sigmoidoscopy, 38563/Bacterial Infection, 38563/Texture of Stool,
38563/Desmopressin Injection, 38563/:PAL-CONSTRAINT, 38563/Factor XIII
concentrate, 38563/Inhalation Anesthesia, 38563/Colonoscopy, 38563/Severe
Minor Wound Bleeding Form (V), 38563/Teething, 38563/Opthalmic Bleeding
Event Form, 38563/Radiation Therapy, 38563/Kidney Stone Removal,
38563/Left Nostril, 38563/REFERENCE-CLASS, 38563/Loacal Pressure,
38563/Chest, 38563/Menstrual Period, 38563/Farm injury, 38563/:DIRECTEDBINARY-RELATION, 38563/Shaving Cut, 38563/Bleeding After Tooth
Extraction, 38563/Horseback injury, 38563/Uterine Ablation,
38563/Cerebral Aneurism, 38563/Ice, 38563/Bleeding From Tongue Form,
38563/Topical Thrombin, 38563/Aspirin Form, 38563/Factor XI concentrate,
38563/Tooth Extraction Form, 38563/Unusual Stool Color Form,
38563/Connective Tissue Assesment Form, 38563/Orbital Bleeding,
38563/NSAID, 38563/Factor VIII Deficiency, 38563/Abnormalities of
Capillaries Form, 38563/Cushing's Syndrome Assesment Form, 38563/Shift in
Body Fat Distribution, 38563/Bandage, 38563/Plasma Transfusion,
38563/Slow Skin Healing, 38563/Delayed Bleeding From Procedure or
Surgery, 38563/Motor vehicle accident injury, 38563/Bronchitis,
38563/:STANDARD-SLOT-CN, 38563/Petechiae, 38563/Umbilical Cord Separation
Form, 38563/Muscle, 38563/CT Scan, 38563/Hematoma, 38563/Relative,
38563/Knee, 38563/Tooth Extraction, 38563/Hematemesis, 38563/Nasal
Packing, 38563/Hemoptysis, 38563/Shaving Cut Form, 38563/Severe Custenous
Symptom Form (V), 38563/Hemorrhage From Trauma, 38563/Localized Bruising
Form, 38563/Gastritis, 38563/MIscarriage, 38563/Fat Deposition on Neck,
38563/Avitene Packing, 38563/Bronchiectasis, 38563/AMICAR,
38563/Postnatal Hemorrhage Form, 38563/Face, 38563/Pregnancy Form,
38563/Fragile Scars, 38563/Factor IX concentrate, 38563/Gingival
Hemorrhage, 38563/Menstruation, 38563/Bleeding From Lips Form,
38563/Induced Delivery, 38563/Hematuria Form, 38563/General Hemarthroses
Form, 38563/Other Minor Cut, 38563/Procedure or Surgery Hemorrhage Form,
38563/Cautery, 38563/Uterine Polyp, 38563/Other Surgery,
38563/Bronchoscopy, 38563/Severe Kidney Disease, 38563/Bullet wound,
38563/Bleeding From Lips, 38563/Per Day, 38563/Factor X Deficiency,
38563/Angiodysplasia, 38563/Menstruation History Form, 38563/Cerebral
Hemorrhage, 38563/Dental Regional Nerve Block, 38563/Age, 38563/Angiomas
Form, 38563/Abdomen Stretch Marks, 38563/Factor VII Deficiency,
38563/:STANDARD-FACET, 38563/Factor VIII, 38563/Gingival Hemorrhage Other
Than with Brushing and Flossing Form, 38563/Unmbilical Cord Stump,
38563/Gauze Packing, 38563/Prenatal, 38563/Sports injury, 38563/Caesarian
Section, 38563/:INSTANCE-ANNOTATION, 38563/MRI, 38563/Other Minor Cut
Form, 38563/Fibring Glue, 38563/Severe Liver Disease, 38563/Molar,
38563/Hematoma Form, 38563/Intravenous Anesthesia, 38563/Viral Infection,
38563/Antibiotics, 38563/Wrist, 38563/NOREFSYS-CLASS, 38563/Epistaxis
Form, 38563/Prothrombin Complex Concentrate, 38563/Tuberculosis,
38563/Dilatation and Curettage, 38563/Frenulum, 38563/Stomach,
38563/Abortion, 38563/General Gingival Hemorrhage Form, 38563/Knife
wound, 38563/Stroke, 38563/Right Nostril, 38563/FORM-CLASS,
38563/Gingival Hemorrhage With Brushing And Flossing Form, 38563/Patient,
38563/Upper Arm, 38563/Delivery Hemorrhage Form, 38563/Aniodysplasia
Form, 38563/Hematemesis Form, 38563/Unsusual Stool Texture Form,
38563/Heavy Flow During Menstruation Form, 38563/Factor XI Deficiency,
38563/Angioma, 38563/Glass wound, 38563/Telangiectasias Form,
38563/Platelet transfusion, 38563/Elbow, 38563/Gastric Ulcer,
38563/Epistaxis, 38563/Venipuncture Form, 38563/Cytoscopy, 38563/Unusual
Skin Texture, 38563/Esophageal Tear, 38563/NSAID Form, 38563/Tooth Loss,
38563/Abnormal Connective Tissue, 38563/Duration Range, 38563/Resurgery,
38563/Platelet Abnormality, 38563/Venipuncture, 38563/Localized
Hemarthroses Form, 38563/Spider Telangiectasias, 38563/Dental Local By
Injection Anesthesia, 38563/Iron Injections, 38563/Recent Bruising Form,
38563/Postnatal, 38563/Cushing's Syndrome, 38563/Back, 38563/Lower Arm,
38563/Factor V Deficiency, 38563/Linear lace-like red marks,
38563/Permanent, 38563/Loose Skin, 38563/Sutures, 38563/von Willebrand
Factor Deficiency, 38563/Physician, 38563/Paper Cut, 38563/Incisor,
38563/Ultrasound, 38563/Other Thrombocytopenia, 38563/Bleeding From
Tongue, 38563/Uterine Fibroids, 38563/Iron Pills, 38563/Circumcision
Form, 38563/Deciduous, 38563/Hematuria, 38563/Duodenal Ulcer,
38563/Hemoptysis Form, 38563/Teething Form, 38563/Severe Epistaxis From
(V), 38563/Double Jointedness, 38563/Rounded Face, 38563/Canine,
38563/Duration, 38563/Immune Thrombocytopenia, 38563/Lips, 38563/Bruising
Event, 38563/Neck, 38563/Factor XIII Deficiency, 38563/Natural or
Developmental Event, 38563/Hemorrhage During Pregnancy, 38563/Bruising
History, 38563/Tranexamic Acid, 38563/Linear Lace-like Red Marks Form,
38563/Scratch, 38563/Other Excessive Hemorrhage, 38563/Trunk, 38563/Oral
Surgery, 38563/Hemathroses, 38563/Esophageal Varices, 38563/Emphysema,
38563/Family Bleeding History Form, 38563/Per Year, 38563/Factor VIIa,
38563/Lower Leg, 38563/Desmopressin Nasal Spray, 38563/Trauma Event Form,
38563/Hysterectomy, 38563/Ankle, 38563/Red Blood Cell Transfusion,
38563/Circumcision, 38563/Thigh]
Ontology hierarchy processed in [00h 00m 03s].
Processing ontology: Experimental Factor Ontology (39885)...
Dumping all the concepts... (1640)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 01m 10s].
Processing ontology: Situation-Based Access Control (39798)...
Dumping all the concepts... (150)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 02s].
Processing ontology: Suggested Ontology for Pharmacogenomics
(39343)...
Dumping all the concepts... (8645)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [00h 12m 00s].
Processing ontology: Vaccine Ontology (39700)...
Dumping all the concepts... (1633)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
,28,29,30,31,32,33,34,35,36,37,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 01m 46s].
Processing ontology: Gene Ontology (39913)...
Dumping all the concepts... (27342)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
Step 3 - Completing PTRs on table OBS_PTRT... ...
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 29m 56s].
Processing ontology: Ontology of Glucose Metabolism Disorder
(39580)...
Dumping all the concepts... (182)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 08s].
Processing ontology: Infectious disease (39501)...
Dumping all the concepts... (152)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 00m 01s].
Processing ontology: Computer-based Patient Record Ontology
(39900)...
Dumping all the concepts... (139)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 03s].
Processing ontology: Amino Acid with Simplified Chinese annotations
(39417)...
Dumping all the concepts... (46)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39546)...
Dumping all the concepts... (14)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: human phenotype ontology (39914)...
Dumping all the concepts... (8972)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,
Step 3 - Completing PTRs on table OBS_PTRT... .
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 09m 35s].
Processing ontology: Comparative Data Analysis Ontology (39879)...
Dumping all the concepts... (125)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 01s].
Processing ontology: Drosophila gross anatomy (39608)...
Dumping all the concepts... (6369)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,
Step 3 - Completing PTRs on table OBS_PTRT... ....
Step 3bis - Completing PTLs on table OBS_PTLT... ...
Ontology hierarchy processed in [08h 39m 34s].
Processing ontology: Sequence types and features (39847)...
Dumping all the concepts... (13)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 00s].
Processing ontology: Phenotypic quality (39886)...
Dumping all the concepts... (1134)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 00m 49s].
Processing ontology: Chemical entities of biological interest
(39895)...
Dumping all the concepts... (20403)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ...
Ontology hierarchy processed in [01h 49m 11s].
Processing ontology: C. elegans gross anatomy (39853)...
Dumping all the concepts... (3715)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... .
Ontology hierarchy processed in [00h 04m 56s].
Hierarchy tables populated in [19h 42m 37s].
*** Populate semantic type table (OBS_STT)...
0 total semantic types added.
Processing ontology: C. elegans phenotype (39854)... 1829 semantic
types added for ontology: 39854.
Processing ontology: Foundational Model of Anatomy (4513)... 78988
semantic types added for ontology: 4513.
Processing ontology: Electrocardiography (ECG) Ontology (39893)...
497 semantic types added for ontology: 39893.
Processing ontology: Mosquito gross anatomy (39331)... 1861
semantic types added for ontology: 39331.
Processing ontology: Ontology for Biomedical Investigations
(39317)... 1364 semantic types added for ontology: 39317.
Processing ontology: Teleost anatomy and development (39892)...
2477 semantic types added for ontology: 39892.
Processing ontology: Evidence codes (39628)... 149 semantic types
added for ontology: 39628.
Processing ontology: PRotein Ontology (PRO) (39891)... 1823
semantic types added for ontology: 39891.
Processing ontology: Ontology of Geographical Region (39577)... 39
semantic types added for ontology: 39577.
Processing ontology: Yeast phenotypes (39909)... 259 semantic types
added for ontology: 39909.
Processing ontology: BioPortal Metadata (39545)... 95 semantic
types added for ontology: 39545.
Processing ontology: Mouse adult gross anatomy (39778)... 2882
semantic types added for ontology: 39778.
Processing ontology: Pathway ontology (39665)... 648 semantic types
added for ontology: 39665.
Processing ontology: NIFSTD (39664)... 12000 semantic types added
for ontology: 39664.
Processing ontology: Gene Regulation Ontology (39624)... 439
semantic types added for ontology: 39624.
Processing ontology: NCI Thesaurus (39478)... 70923 semantic types
added for ontology: 39478.
Processing ontology: Mammalian phenotype (39859)... 6741 semantic
types added for ontology: 39859.
Processing ontology: DermLex: The Dermatology Lexicon (39815)...
6101 semantic types added for ontology: 39815.
Processing ontology: Environment Ontology (39858)... 1231 semantic
types added for ontology: 39858.
Processing ontology: Subcellular Anatomy Ontology (SAO) (14391)...
821 semantic types added for ontology: 14391.
Processing ontology: Mosquito insecticide resistance (39915)...
4309 semantic types added for ontology: 39915.
Processing ontology: Human disease (39857)... 12311 semantic types
added for ontology: 39857.
Processing ontology: Sample processing and separation techniques
(39509)... 194 semantic types added for ontology: 39509.
Processing ontology: Ascomycete phenotype ontology (39907)... 278
semantic types added for ontology: 39907.
Processing ontology: Protein-protein interaction (39508)... 906
semantic types added for ontology: 39508.
Processing ontology: Ontology for Genetic Interval (39578)... 202
semantic types added for ontology: 39578.
Processing ontology: NanoParticle Ontology (39717)... 919 semantic
types added for ontology: 39717.
Processing ontology: Fungal gross anatomy (39704)... 70 semantic
types added for ontology: 39704.
Processing ontology: Ontology for disease genetic investigation
(39579)... 388 semantic types added for ontology: 39579.
Processing ontology: BIRNLex (29684)... 3580 semantic types added
for ontology: 29684.
Processing ontology: Teleost taxonomy (39905)... 36596 semantic
types added for ontology: 39905.
Processing ontology: Biomedical Resource Ontology (39521)... 407
semantic types added for ontology: 39521.
Processing ontology: Bleeding History Phenotype (38563)... 302
semantic types added for ontology: 38563.
Processing ontology: Experimental Factor Ontology (39885)... 1640
semantic types added for ontology: 39885.
Processing ontology: Situation-Based Access Control (39798)... 150
semantic types added for ontology: 39798.
Processing ontology: Suggested Ontology for Pharmacogenomics
(39343)... 8645 semantic types added for ontology: 39343.
Processing ontology: Vaccine Ontology (39700)... 1633 semantic
types added for ontology: 39700.
Processing ontology: Gene Ontology (39913)... 27342 semantic types
added for ontology: 39913.
Processing ontology: Ontology of Glucose Metabolism Disorder
(39580)... 182 semantic types added for ontology: 39580.
Processing ontology: Infectious disease (39501)... 152 semantic
types added for ontology: 39501.
Processing ontology: Computer-based Patient Record Ontology
(39900)... 139 semantic types added for ontology: 39900.
Processing ontology: Amino Acid with Simplified Chinese annotations
(39417)... 46 semantic types added for ontology: 39417.
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39546)... 14 semantic types added for ontology: 39546.
Processing ontology: human phenotype ontology (39914)... 8972
semantic types added for ontology: 39914.
Processing ontology: Comparative Data Analysis Ontology (39879)...
125 semantic types added for ontology: 39879.
Processing ontology: Drosophila gross anatomy (39608)... 6369
semantic types added for ontology: 39608.
Processing ontology: MaHCO - An MHC Ontology (39804)... 6720
semantic types added for ontology: 39804.
Processing ontology: Plant structure (39724)... 809 semantic types
added for ontology: 39724.
Processing ontology: FlyBase Controlled Vocabulary (39366)... 686
semantic types added for ontology: 39366.
Processing ontology: Sequence types and features (39847)... 13
semantic types added for ontology: 39847.
Processing ontology: Zebrafish anatomy and development (39496)...
2219 semantic types added for ontology: 39496.
Processing ontology: Units of measurement (39649)... 1392 semantic
types added for ontology: 39649.
Processing ontology: Mouse pathology (39587)... 588 semantic types
added for ontology: 39587.
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39549)... 15 semantic types added for ontology: 39549.
Processing ontology: Parasite Life Cycle (39544)... 41 semantic
types added for ontology: 39544.
Processing ontology: Phenotypic quality (39886)... 1134 semantic
types added for ontology: 39886.
Processing ontology: NCBI organismal classification (38802)...
455536 semantic types added for ontology: 38802.
Processing ontology: Chemical entities of biological interest
(39895)... 20403 semantic types added for ontology: 39895.
Processing ontology: C. elegans gross anatomy (39853)... 3715
semantic types added for ontology: 39853.
Processing ontology: RadLex (21275)... 11593 semantic types added
for ontology: 21275.
811902 total semantic types added.
0 total semantic types added.
811902 total semantic types added in [00h 09m 57s].
*** Populate mapping table (OBS_MAPT)...
------------------------------ MANUALLY STOPED TO EXECUTE
removeOntologyDuplicate FIRST TO WIN SOME TIME---------------------*** Remove duplicate ontologies from OBS tables...
Removing ontology 39071 and dependencies from the OBS DB...
Ontology 39071 and dependencies removed from the OBS DB.
Removing ontology 39284 and dependencies from the OBS DB...
Ontology 39284 and dependencies removed from the OBS DB.
Removing ontology 39025 and dependencies from the OBS DB...
Ontology 39025 and dependencies removed from the OBS DB.
Removing ontology 39576 and dependencies from the OBS DB...
Ontology 39576 and dependencies removed from the OBS DB.
Removing ontology 39708 and dependencies from the OBS DB...
Ontology 39708 and dependencies removed from the OBS DB.
Removing ontology 38703 and dependencies from the OBS DB...
Ontology 38703 and dependencies removed from the OBS DB.
Removing ontology 39208 and dependencies from the OBS DB...
Ontology 39208 and dependencies removed from the OBS DB.
Removing ontology 14174 and dependencies from the OBS DB...
Ontology 14174 and dependencies removed from the OBS DB.
Removing ontology 39769 and dependencies from the OBS DB...
Ontology 39769 and dependencies removed from the OBS DB.
Removing ontology 38819 and dependencies from the OBS DB...
Ontology 38819 and dependencies removed from the OBS DB.
Removing ontology 3134 and dependencies from the OBS DB...
Ontology 3134 and dependencies removed from the OBS DB.
Removing ontology 39658 and dependencies from the OBS DB...
Ontology 39658 and dependencies removed from the OBS DB.
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
Removing
Ontology
ontology 39762 and dependencies from the OBS DB...
39762 and dependencies removed from the OBS DB.
ontology 39531 and dependencies from the OBS DB...
39531 and dependencies removed from the OBS DB.
ontology 37575 and dependencies from the OBS DB...
37575 and dependencies removed from the OBS DB.
ontology 39318 and dependencies from the OBS DB...
39318 and dependencies removed from the OBS DB.
ontology 39823 and dependencies from the OBS DB...
39823 and dependencies removed from the OBS DB.
ontology 39692 and dependencies from the OBS DB...
39692 and dependencies removed from the OBS DB.
ontology 39002 and dependencies from the OBS DB...
39002 and dependencies removed from the OBS DB.
ontology 39319 and dependencies from the OBS DB...
39319 and dependencies removed from the OBS DB.
ontology 39242 and dependencies from the OBS DB...
39242 and dependencies removed from the OBS DB.
ontology 39320 and dependencies from the OBS DB...
39320 and dependencies removed from the OBS DB.
ontology 39235 and dependencies from the OBS DB...
39235 and dependencies removed from the OBS DB.
ontology 39203 and dependencies from the OBS DB...
39203 and dependencies removed from the OBS DB.
ontology 39175 and dependencies from the OBS DB...
39175 and dependencies removed from the OBS DB.
ontology 39222 and dependencies from the OBS DB...
39222 and dependencies removed from the OBS DB.
ontology 39662 and dependencies from the OBS DB...
39662 and dependencies removed from the OBS DB.
ontology 39734 and dependencies from the OBS DB...
39734 and dependencies removed from the OBS DB.
ontology 39051 and dependencies from the OBS DB...
39051 and dependencies removed from the OBS DB.
ontology 39824 and dependencies from the OBS DB...
39824 and dependencies removed from the OBS DB.
ontology 39288 and dependencies from the OBS DB...
39288 and dependencies removed from the OBS DB.
ontology 39225 and dependencies from the OBS DB...
39225 and dependencies removed from the OBS DB.
ontology 39255 and dependencies from the OBS DB...
39255 and dependencies removed from the OBS DB.
ontology 39277 and dependencies from the OBS DB...
39277 and dependencies removed from the OBS DB.
ontology 39715 and dependencies from the OBS DB...
39715 and dependencies removed from the OBS DB.
ontology 39728 and dependencies from the OBS DB...
39728 and dependencies removed from the OBS DB.
ontology 39278 and dependencies from the OBS DB...
39278 and dependencies removed from the OBS DB.
ontology 38835 and dependencies from the OBS DB...
38835 and dependencies removed from the OBS DB.
ontology 38763 and dependencies from the OBS DB...
38763 and dependencies removed from the OBS DB.
Removing ontology 39354 and dependencies from the OBS DB...
Ontology 39354 and dependencies removed from the OBS DB.
Removing ontology 39310 and dependencies from the OBS DB...
Ontology 39310 and dependencies removed from the OBS DB.
Removing ontology 39718 and dependencies from the OBS DB...
Ontology 39718 and dependencies removed from the OBS DB.
Removing ontology 3026 and dependencies from the OBS DB...
Ontology 3026 and dependencies removed from the OBS DB.
Removing ontology 39228 and dependencies from the OBS DB...
Ontology 39228 and dependencies removed from the OBS DB.
Removing ontology 39797 and dependencies from the OBS DB...
Ontology 39797 and dependencies removed from the OBS DB.
Removing ontology 38847 and dependencies from the OBS DB...
Ontology 38847 and dependencies removed from the OBS DB.
Removing ontology 39829 and dependencies from the OBS DB...
Ontology 39829 and dependencies removed from the OBS DB.
Removing ontology 38483 and dependencies from the OBS DB...
Ontology 38483 and dependencies removed from the OBS DB.
48 ontologies removed in [01h 48m 54s].
Execution done in: 01 hours, 48 minutes, 54
seconds.(6534550ms).
-------------------------- RESUME WITH LATEST UPDATE OF ONTOLOGIES FORM
BP (May 4th 2009)
2 ontologies added.
*** Populate concept tables (OBS_TT & OBS_CT) and
directParents/directChildren (OBS_ISAPT)...
*** Populate concept tables (OBS_TT & OBS_CT) and
directParents/directChildren (OBS_ISAPT) with BioPortal...
Processing ontology: Mosquito insecticide resistance (39918)...
4309 concepts added in [00h 12m 47s] for ontology: 39918.
Processing ontology: Gene Ontology (39917)... 27342 concepts added
in [01h 28m 23s] for ontology: 39917.
2 ontolgies added.
31651 total concepts added in [01h 41m 10s].
*** Populate hierarchy tables (OBS_ISAPT, OBS_PTRT, OBS_PTLT, et Lcui
tables)...
Processing ontology: Mosquito insecticide resistance (39918)...
Dumping all the concepts... (4309)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT... i=1,2,3,4,5,6,7,8,9,
Step 3 - Completing PTRs on table OBS_PTRT...
Step 3bis - Completing PTLs on table OBS_PTLT...
Ontology hierarchy processed in [00h 03m 23s].
Processing ontology: Gene Ontology (39917)...
Dumping all the concepts... (27342)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
Step 3 - Completing PTRs on table OBS_PTRT... ...
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 28m 57s].
Hierarchy tables populated in [01h 32m 20s].
*** Populate semantic type table (OBS_STT)...
0 total semantic types added.
Processing ontology: Mosquito insecticide resistance (39918)...
4309 semantic types added for ontology: 39918.
Processing ontology: Gene Ontology (39917)... 27342 semantic types
added for ontology: 39917.
31651 total semantic types added.
0 total semantic types added.
31651 total semantic types added in [00h 00m 17s].
-------------------- MANUALLY STOPPED AFTER MAPPING DUMPING BUGS---------------------------*** Remove duplicate ontologies from OBS tables...
Removing ontology 39915 and dependencies from the OBS DB...
Ontology 39915 and dependencies removed from the OBS DB.
Removing ontology 39913 and dependencies from the OBS DB...
Ontology 39913 and dependencies removed from the OBS DB.
2 ontologies removed in [00h 09m 07s].
------------------- RESUMED AFTER AFTER MAPPING DUMPING BUGS FIXES ------------------------------*** Populate semantic type table (OBS_STT)...
0 total semantic types added.
Processing ontology: Lipid Ontology (39503)... 715 semantic types
added for ontology: 39503.
715 total semantic types added.
0 total semantic types added.
715 total semantic types added in [00h 00m 00s].
*** Populate mapping table (OBS_MAPT)...
Processing ontology: C. elegans phenotype (39854)... 0 mappings
added for ontology: 39854.
Processing ontology: Foundational Model of Anatomy (4513)...
------------------- RESUMED AFTER AFTER BP MAPPING TABLE INDEX CRETAED ------------------------------*** Populate mapping table (OBS_MAPT)...
Processing ontology: Electrocardiography (ECG) Ontology (39893)...
0 mappings added for ontology: 39893.
Processing ontology: Mosquito gross anatomy (39331)... 0 mappings
added for ontology: 39331.
Processing ontology: Foundational Model of Anatomy (4513)... 0
mappings added for ontology: 4513.
Processing ontology: Ontology for Biomedical Investigations
(39317)... 0 mappings added for ontology: 39317.
Processing ontology: Teleost anatomy and development (39892)...
------------------- RESUMED AFTER AFTER MAPPING DUMPING BUGS FIXES ------------------------------*** Populate mapping table (OBS_MAPT)...
Processing ontology: Teleost anatomy and development (39892)... 0
mappings added for ontology: 39892.
Processing ontology: Cell type (39004)... 10 mappings added for
ontology: 39004.
Processing ontology: Medaka fish anatomy and development (3093)...
0 mappings added for ontology: 3093.
Processing ontology: Evidence codes (39628)... 0 mappings added for
ontology: 39628.
Processing ontology: Biological imaging methods (3057)... 0
mappings added for ontology: 3057.
Processing ontology: PRotein Ontology (PRO) (39891)... 0 mappings
added for ontology: 39891.
Processing ontology: Ontology of Geographical Region (39577)... 0
mappings added for ontology: 39577.
Processing ontology: Pathogen transmission (39223)... 0 mappings
added for ontology: 39223.
Processing ontology: Yeast phenotypes (39909)... 0 mappings added
for ontology: 39909.
Processing ontology: BioPortal Metadata (39545)... 0 mappings added
for ontology: 39545.
Processing ontology: Tick gross anatomy (38366)... 0 mappings added
for ontology: 38366.
Processing ontology: SNP-Ontology (39215)... 0 mappings added for
ontology: 39215.
Processing ontology: Mouse adult gross anatomy (39778)...
(---------------mappings bugs move to other log)
2585 mappings added for ontology: 39778.
Processing ontology: Pathway ontology (39665)... 0 mappings added
for ontology: 39665.
Processing ontology: Cell Cycle Ontology (H. sapiens) (36417)... 0
mappings added for ontology: 36417.
Processing ontology: Spatial Ontology (38996)... 0 mappings added
for ontology: 38996.
Processing ontology: NIFSTD (39664)... 0 mappings added for
ontology: 39664.
Processing ontology: Mass spectrometry (39281)... 0 mappings added
for ontology: 39281.
Processing ontology: Sequence Ontology (36782)... 0 mappings added
for ontology: 36782.
Processing ontology: Gene Regulation Ontology (39624)... 0 mappings
added for ontology: 39624.
Processing ontology: Mammalian phenotype (39859)... 0 mappings
added for ontology: 39859.
Processing ontology: NCI Thesaurus (39478)...
(---------------mappings bugs move to other log)
2413 mappings added for ontology: 39478.
Processing ontology: Rat Strain Ontology (39234)... 0 mappings
added for ontology: 39234.
Processing ontology: Cancer Research and Management ACGT Master
Ontology (38787)... 0 mappings added for ontology: 38787.
Processing ontology: Amino Acid (4519)... 0 mappings added for
ontology: 4519.
Processing ontology: Common Anatomy Reference Ontology (13305)... 0
mappings added for ontology: 13305.
Processing ontology: DermLex: The Dermatology Lexicon (39815)... 0
mappings added for ontology: 39815.
Processing ontology: Environment Ontology (39858)... 0 mappings
added for ontology: 39858.
Processing ontology: Subcellular Anatomy Ontology (SAO) (14391)...
0 mappings added for ontology: 14391.
Processing ontology: Family Health History Ontology (38631)... 0
mappings added for ontology: 38631.
Processing ontology: Human disease (39857)...
(---------------mappings bugs move to other log)
14472 mappings added for ontology: 39857.
Processing ontology: Sample processing and separation techniques
(39509)... 0 mappings added for ontology: 39509.
Processing ontology: C. elegans development (25148)... 0 mappings
added for ontology: 25148.
Processing ontology: Protein-protein interaction (39508)... 0
mappings added for ontology: 39508.
Processing ontology: Ascomycete phenotype ontology (39907)... 0
mappings added for ontology: 39907.
Processing ontology: African Traditional Medicine (32145)... 0
mappings added for ontology: 32145.
Processing ontology: Mouse gross anatomy and development (13323)...
0 mappings added for ontology: 13323.
Processing ontology: Ontology for Genetic Interval (39578)... 0
mappings added for ontology: 39578.
Processing ontology: NanoParticle Ontology (39717)...
(---------------mappings bugs move to other log)
0 mappings added for ontology: 39717.
Processing ontology: Fungal gross anatomy (39704)... 0 mappings
added for ontology: 39704.
Processing ontology: Ontology of Physics for Biology (39001)... 0
mappings added for ontology: 39001.
Processing ontology: Drosophila development (39019)... 0 mappings
added for ontology: 39019.
Processing ontology: Ontology for disease genetic investigation
(39579)... 0 mappings added for ontology: 39579.
Processing ontology: Proteomics data and process provenance
(13386)... 0 mappings added for ontology: 13386.
Processing ontology: Multiple alignment (3083)... 0 mappings added
for ontology: 3083.
Processing ontology: BIRNLex (29684)... 0 mappings added for
ontology: 29684.
Processing ontology: Teleost taxonomy (39905)... 0 mappings added
for ontology: 39905.
Processing ontology: Pseudogene (38873)... 0 mappings added for
ontology: 38873.
Processing ontology: Biomedical Resource Ontology (39521)... 1
mappings added for ontology: 39521.
Processing ontology: Bleeding History Phenotype (38563)... 0
mappings added for ontology: 38563.
Processing ontology: Experimental Factor Ontology (39885)... 0
mappings added for ontology: 39885.
Processing ontology: Amphibian gross anatomy (37911)... 0 mappings
added for ontology: 37911.
Processing ontology: Situation-Based Access Control (39798)... 0
mappings added for ontology: 39798.
Processing ontology: Cardiac Electrophysiology Ontology (39038)...
0 mappings added for ontology: 39038.
Processing ontology: Suggested Ontology for Pharmacogenomics
(39343)... 0 mappings added for ontology: 39343.
Processing ontology: Vaccine Ontology (39700)... 0 mappings added
for ontology: 39700.
Processing ontology: BioTop (38828)... 0 mappings added for
ontology: 38828.
Processing ontology: Xenopus anatomy and development (39046)... 0
mappings added for ontology: 39046.
Processing ontology: Ontology of Glucose Metabolism Disorder
(39580)... 0 mappings added for ontology: 39580.
Processing ontology: Physico-chemical process (13397)... 0 mappings
added for ontology: 13397.
Processing ontology: Infectious disease (39501)... 0 mappings added
for ontology: 39501.
Processing ontology: Epoch Clinical Trial Ontologies (8056)... 0
mappings added for ontology: 8056.
Processing ontology: Computer-based Patient Record Ontology
(39900)... 0 mappings added for ontology: 39900.
Processing ontology: Basic Vertebrate Anatomy (4531)... 1 mappings
added for ontology: 4531.
Processing ontology: Amino Acid with Simplified Chinese annotations
(39417)... 0 mappings added for ontology: 39417.
Processing ontology: Galen (4525)...
(---------------mappings bugs move to other log)
246 mappings added for ontology: 4525.
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39546)... 0 mappings added for ontology: 39546.
Processing ontology: International Classification of Diseases
(35686)... 0 mappings added for ontology: 35686.
Processing ontology: Human developmental anatomy, abstract version
(13352)... 0 mappings added for ontology: 13352.
Processing ontology: Microarray experimental conditions (38801)...
0 mappings added for ontology: 38801.
Processing ontology: Lipid Ontology (39503)... 0 mappings added for
ontology: 39503.
Processing ontology: Comparative Data Analysis Ontology (39879)...
0 mappings added for ontology: 39879.
Processing ontology: Cell Cycle Ontology (S. pombe) (36430)... 0
mappings added for ontology: 36430.
Processing ontology: Drosophila gross anatomy (39608)... 0 mappings
added for ontology: 39608.
Processing ontology: Human developmental anatomy, timed version
(13356)... 0 mappings added for ontology: 13356.
Processing ontology: MaHCO - An MHC Ontology (39804)... 0 mappings
added for ontology: 39804.
Processing ontology: Plant structure (39724)... 0 mappings added
for ontology: 39724.
Processing ontology: FlyBase Controlled Vocabulary (39366)... 0
mappings added for ontology: 39366.
Processing ontology: Sequence types and features (39847)... 0
mappings added for ontology: 39847.
Processing ontology: Zebrafish anatomy and development (39496)...
(---------------mappings bugs move to other log)
556 mappings added for ontology: 39496.
Processing ontology: Spider Ontology (38644)... 0 mappings added
for ontology: 38644.
Processing ontology: Units of measurement (39649)... 0 mappings
added for ontology: 39649.
Processing ontology: Mouse pathology (39587)... 0 mappings added
for ontology: 39587.
Processing ontology: Protein Ontology (3905)... 0 mappings added
for ontology: 3905.
Processing ontology: Cell Cycle Ontology (S. cerevisiae) (36425)...
0 mappings added for ontology: 36425.
Processing ontology: Plant growth and developmental stage
(37419)... 0 mappings added for ontology: 37419.
Processing ontology: Proteomics Pipeline Infrastructure for CPTAC
(39549)... 0 mappings added for ontology: 39549.
Processing ontology: Dictyostelium discoideum anatomy (36622)... 0
mappings added for ontology: 36622.
Processing ontology: Cell Cycle Ontology (A. thaliana) (38550)... 0
mappings added for ontology: 38550.
Processing ontology: Plant environmental conditions (39183)... 0
mappings added for ontology: 39183.
Processing ontology: Parasite Life Cycle (39544)... 0 mappings
added for ontology: 39544.
Processing ontology: Phenotypic quality (39886)... 0 mappings added
for ontology: 39886.
Processing ontology: NCBI organismal classification (38802)... 0
mappings added for ontology: 38802.
Processing ontology: Chemical entities of biological interest
(39895)... 3 mappings added for ontology: 39895.
Processing ontology: C. elegans gross anatomy (39853)... 0 mappings
added for ontology: 39853.
Processing ontology: Fly taxonomy (13342)... 0 mappings added for
ontology: 13342.
Processing ontology: RadLex (21275)... 1 mappings added for
ontology: 21275.
Processing ontology: Cereal plant trait (31197)... 3 mappings added
for ontology: 31197.
20291 total mappings added in [01h 48m 26s].
*** Remove duplicate ontologies from OBS tables...
0 ontologies removed in [00h 00m 23s].
Execution done in: 01 hours, 48 minutes, 53
seconds.(6533695ms).
----------------------- RESUME FOR MAPPINGS OF 4 LAST ONTOLOGIES
-----------------
-------
Ontology <Ontology of Clinical Research (OCRe)> (23466) added to the set
of ontologies accessed by OBS_OATOOL_42f_BIOPORTAL_bioportal.
Ontology <Gene Ontology> (39917) added to the set of ontologies accessed
by OBS_OATOOL_42f_BIOPORTAL_bioportal.
Ontology <Mosquito insecticide resistance> (39918) added to the set of
ontologies accessed by OBS_OATOOL_42f_BIOPORTAL_bioportal.
Ontology <human phenotype ontology> (39914) added to the set of
ontologies accessed by OBS_OATOOL_42f_BIOPORTAL_bioportal.
*** Populate mapping table (OBS_MAPT)...
Processing ontology: Ontology of Clinical Research (OCRe)
(23466)... 0 mappings added for ontology: 23466.
Processing ontology: Gene Ontology (39917)... 1 mappings added for
ontology: 39917.
Processing ontology: Mosquito insecticide resistance (39918)... 0
mappings added for ontology: 39918.
Processing ontology: human phenotype ontology (39914)... 0 mappings
added for ontology: 39914.
1 total mappings added in [00h 00m 19s].
Execution done in: 00 hours, 00 minutes, 19
seconds.(19832ms).
-------------------- LAST RUN TO ADD NCIT 13578 ------------------------Ontology <NCI Thesaurus> (13578) added to the set of ontologies accessed
by OBS_OATOOL_fcb_BIOPORTAL_bioportal.
*** Populate ontology table (OBS_OT)... 1 ontologies added.
*** Populate concept tables (OBS_TT & OBS_CT) and
directParents/directChildren (OBS_ISAPT)...
0 ontologies added.
*** Populate concept tables (OBS_TT & OBS_CT) and
directParents/directChildren (OBS_ISAPT) with BioPortal...
Processing ontology: NCI Thesaurus (13578)... 2009-05-05
15:35:19,298 WARN [org.apache.commons.httpclient.HttpMethodBase] - Going
to buffer response body of large or unknown size. Using
getResponseBodyAsStream instead is recommended.
com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for
column 'localConceptID' at row 1
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry: [13578/Autologous-Dendritic-Cells_Candida-Albicans-SkinTest-Reagent_CD40-Ligand_gp100-Antigen_Interferon-Gamma_Interleukin4_MART-1-Antigen_Sargramostim_Tyrosinase-Peptide, 13578/NonCurrent_Chemotherapy_Regimen_or_Association, 1]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry: [13578/Autologous-Dendritic-Cells_Candida-Albicans-SkinTest-Reagent_CD40-Ligand_gp100-Antigen_Interferon-Gamma_Interleukin4_MART-1-Antigen_Sargramostim_Tyrosinase-Peptide, 13578, false]
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry:
[13578/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
13578/Adverse_Event_Associated_with_Infection, 1]
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry:
[13578/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 13578/Adverse_Event_Associated_with_Infection, 1]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
13578, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Febrile_Neutropenia_without_Clinically_or_Microbiologically_Docume
nted_Infection_with_Absolute_Neutrophil_Count_Less_Than_1_X_10e9_per_Lite
r_and_Temperature_Greater_Than_or_Equal_to_38_Point_5_Degrees_Celsius,
13578, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 13578, false]
ConceptEntry:
[13578/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 13578, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Infection_Adverse_Event_Documented_Clinically_or_Microbiologically
_with_Grade_3_or_4_Neutrophils_Absolute_Neutrophil_Count_Less_Than_1_X_10
e9_per_Liter, 13578, false]
** PROBLEM ** Cannot add an entry on table OBS_ISAPT
IsaParentEntry:
[13578/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 13578/Retired_Concepts, 1]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 13578, false]
ConceptEntry:
[13578/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 13578, false]
ConceptEntry:
[13578/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 13578, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 13578, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 13578, false]
** PROBLEM ** Cannot add an entry on table OBS_CT
ConceptEntry:
[13578/Mouse_Endometrioid_Ovarian_Adenofibroma_of_Borderline_Malignancy_M
ouse_Endometrioid_Ovarian_Cystadenofibroma_of_Borderline_Malignancy_with_
Squamous_Differentiation, 13578, false]
66330 concepts added in [01h 42m 16s] for ontology: 13578.
1 ontolgies added.
0 ontologies added.
66330 total concepts added in [01h 42m 16s].
*** Populate hierarchy tables (OBS_ISAPT, OBS_PTRT, OBS_PTLT) for UMLS
only...
Hierarchy tables (UMLS) populated in [00h 00m 00s].
*** Populate hierarchy tables (OBS_ISAPT, OBS_PTRT, OBS_PTLT, et Lcui
tables)...
Processing ontology: NCI Thesaurus (13578)...
Dumping all the concepts... (66330)
Step 1 - Computing the direct children and filling the
tables...
Step 2 - Recursion on table OBS_ISAPT...
i=1,2,3,4,5,6,7,8,9,10,11,12,13,
Step 3 - Completing PTRs on table OBS_PTRT... ..
Step 3bis - Completing PTLs on table OBS_PTLT... ..
Ontology hierarchy processed in [01h 22m 46s].
Hierarchy tables populated in [01h 22m 46s].
*** Populate semantic type table (OBS_STT)...
0 total semantic types added.
Processing ontology: NCI Thesaurus (13578)... 66330 semantic types
added for ontology: 13578.
66330 total semantic types added.
0 total semantic types added.
66330 total semantic types added in [00h 00m 36s].
*** Populate mapping table (OBS_MAPT)...
Processing ontology: NCI Thesaurus (13578)...
(---------------mappings bugs move to other log)
2415 mappings added for ontology: 13578.
2415 total mappings added in [00h 09m 08s].
Dictionary file OBS_DICO_fe30_MGREP.txt generated.
Dictionary file OBS_DICO_fe30_CMP_MGREP.txt generated.
Execution done in: 03 hours, 15 minutes, 41
seconds.(11741615ms).