Repository notes
Started: 2/28/2011
The goal is a distributed database of images, biological data and models. The hope is that if the files
are adequately annotated, using an agreed upon set of reference ontologies, then the distributed
files can be located via a Google search. The user should not need to know where the files are
located. Furthermore, the annotation syntax should be as non-restrictive as possible and annotation
of a file should not change the usability of the file for its original porpose.
Longer range goals might include annotation styles linking annotations to entities in the data file.
For example, in a CC3D model linking cell names and/or type IDs to annotations. Annotations in an
SBML file that link variable names to protein names.
File and data types:
Major issue is that the file type has to be "crawlable" and "indexable" by Google. File types to try
include:
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Any plain text files including computational scripts in python, C++ etc.
Tab or csv data table files containing numeric values (e.g., from ToxCast, a high throughput
assay, or an archive of common physiochemical parameters like affinity constants, diffusion
rates and the like).
MSWord, PowerPoint and PDF files.
HTML files.
Images (jpg, gif …) either as photographs (or micrographs) of tissues, cells etc. or images
generated as output of a modeling program.
Movies of tissues, cells etc. or images generated as from the output of a modeling program.
For the image type of files it would be nice if Google would index the file format's native annotation
block. That would allow the annotation to actually live in the file. (See the file
somatogenesis_image_CC3D_model.jpg for an example.) Unfortunately, it doesn't look like Google
does that. To associate annotation with an image file we need to place both in an HTML (or PDF or
…) file.
Annotations:
The goal is to include the annotation without interfering with the native file format. Annotations in
code or script files should live inside comment delimiters suitable for the particular language. In
non-code files (like HTML, word, csv) this isn't as much of an issue. Major issue is that there needs
to be an agreed upon set of reference ontologies so that end users know which ontologies to search
for query terms. A secondary issue is that a user friendly tool for finding terms in the reference
ontologies would be very helpful.
Possible Reference Ontologies:
Major issue is multi-species requirements. FMA is human can it be adequately used for other
species? In some cases yes, in many cases no.
Ontologies / vocabularies searchable by the querying tools marked with *.
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Mammalian body parts, locations and processes: FMA*
(http://sig.biostr.washington.edu/projects/fm/FME/index.html)
Non-mammalian body parts: ?
Gene Processes: GO*
(http://amigo.geneontology.org/cgi-bin/amigo/go.cgi)
Gene and protein names: PRO*
(http://pir.georgetown.edu/pro/)
Small molecules: ChEBI*
(http://www.ebi.ac.uk/chebi/)
Images: FBbi*
(http://www.obofoundry.org/cgi-bin/detail.cgi?id=image)
Experimental descriptions: ?
Model descriptions: EDAM*
Diseases: ?
Catch-all Reference vocabulary: MeSH
(http://www.nlm.nih.gov/mesh/MBrowser.html)
Another Catch-all Reference Ontology: UMLS
(http://www.nlm.nih.gov/research/umls/ don't know of any online search engines.)
Possible user tools for querying the reference ontologies:
http://www.ebi.ac.uk/ontology-lookup/ (doesn't include UMLS or MeSH!)
http://bioportal.bioontology.org/
Annotation Style:
The key requirement is that the annotation contains the terms, IDs and reference ontology
identifier. For example "FMA:82840 embryonic cell" identifies the ontology (FMA), ID (82840) and
the term name ("embryonic cell"). There should be a unique ontology identifier for the typical
ontologies so that the ID and ontology can be closely linked, perhaps to a single "word" level, such
as "FMA:82840". An explicit listing of the ontologies being used might also be useful. It may be
advantageous to have a text template that lists the major types of annotations that might be
included along with the suitable reference ontology names. The template is not part of the data
structure, it is simply meant to help the annotator work through the process in an orderly fashion.
Major sections of the annotation template might be something along the lines of:
1. Process being modeled/studied (examples: tumor growth, immune response,
embryogenesis)
2. Tissues in the model/system (examples: liver, mammary tumor)
3. Cells in the model/system (examples: macrophage, neuron, epithelium)
4. Non-cell structures in the model/system (examples: bone, basement membrane)
5. Genes and gene products in the model system (examples: VEGF-A, IL-1b)
6. Molecules not covered by 5. (examples: oxygen, glucose, potassium ions)
7. Processes and behaviors of the things (cells, genes, tissues) in the model/system (examples:
gene expression, cell growth, division and death, diffusion)
Some annotated files:
Jpeg image from Julio & Susan’s poster of somitogenesis. Annotations added to the jpeg file
somitogenesis_image.jpg:
Somitogenesis image
Foundational Model of Anatomy FMA:
FMA:69068 embryo
FMA:82840 embryonic cell
Gene Ontology GO:
GO:0009790 embryogenesis
GO:0009792 embryo development ending in birth or egg hatching
GO:0016055 Wnt receptor signaling pathway
Protein Ontology PRO:
PRO:000017443 protein Wnt-3a
Biological Imaging Methods FBbi:
FBbi:00000265 micrograph
MeSH:A16.504.660.750 somites
HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY
Indiana University Bloomington
University of Washington
CC3D (CompuCell3D) Result Image CC3D_somitogenesis_image.jpg:
Somitogenesis computational model image
Foundational Model of Anatomy FMA:
FMA:69068 embryo
FMA:82840 embryonic cell
Gene Ontology GO:
GO:0009790 embryogenesis
GO:0009792 embryo development ending in birth or egg hatching
GO:0016055 Wnt receptor signaling pathway
Protein Ontology PRO:
PRO:000017443 protein Wnt-3a
EMBRACE Ontology for Data and Methods EDAM:
EDAM:0000950 Biological model
Medical Subject Heading MeSH:
MeSH:E05.599 Models, Theoretical
MeSH:E05.599.395 Models, Biological
MeSH:L01.224.160 Computer Simulation
MeSH:A16.504.660.750 somites
Authors:
Susan Hester, Julio Belmonte
Indiana University, Bloomington
Computational Platform:
CompuCell3D CC3D
HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY
Indiana University Bloomington
University of Washington
MP4 Movie file: Crawling_Neutrophil_chasing_bacterium.mp4
Neutrophil chasing a bacterium
UniProt Taxonomy Database NEWT:
NEWT:2 Bacteria
Cell Type Ontology CL:
CL:0000775 neutrophil "polynuclear neutrophilic leucocyte" neutrocyte
Foundational Model of Anatomy FMA:
FMA:62860 "Polymorphonuclear leukocyte"
FMA:82840 embryonic cell
Gene Ontology GO:
GO:0006909 phagocytosis
GO:0060326 "cell chemotaxis"
GO:0048870 "cell motility"
Crawling_Neutrophil_chasing_bacter
Protein Ontology PRO:
Biological Imaging Methods FBbi:
FBbi:00000265 micrograph
FBbi:00000267 animation
HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY
Indiana University Bloomington
University of Washington
Current file list at IU:
8 March 2011 4:38 PM
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0_Read_me.html
3D_multi-cell_simulation_of_tumor_growth_and_angiogenesis.html
3D_multi-cell_simulation_of_tumor_growth_and_angiogenesis.txt
BIOMD0000000201.xml
Crawling_Neutrophil_chasing_bacterium.mp4
Crawling_Neutrophil_chasing_bacterium_annot.wmv
Crawling_Neutrophil_chasing_bacterium_annotation.html
JimsStyle.css
Repository_notes.docx
document_list_IU.html
somitogenesis_CC3D_script.txt
somitogenesis_image.jpg
somitogenesis_image_CC3D_model.jpg
somitogenesis_image_CC3D_model_annotation.html
somitogenesis_image_annotation.html
3/8/2011
Google finds the pages using, e.g., "CHEBIO:15379 cc3d herbs and jims …"
But problem with the svn paths FIXED
MeSH terms used for typical biomodels.
Abbas et al. Tumor
Niko et al. Tumor
Cardiac ventricular action
potential
PLoS One. 2009 Oct 16;4(10):e7190.
PLoS One. 2010 May 26;5(5):e10641.
Circ Res. 1994 Jun;74(6):1071-96.
"3D multi-cell simulation of
tumor growth and
angiogenesis" Shirinifard A,
Gens JS, Zaitlen BL, Popławski
NJ, Swat M, Glazier JA.
"Front instabilities and
invasiveness of simulated 3D
avascular tumors" Poplawski
NJ, Shirinifard A, Agero U, Gens
JS, Swat M, Glazier JA.
"A dynamic model of the
cardiac ventricular action
potential. I. Simulations of ionic
currents and concentration
changes" Luo CH, Rudy Y.
MH
MH
MH
MH
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MH
MH
MH
MH
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MH
MH
MH
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MH
MH
MH
MH
MH
MH
MH
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MH
MH
MH
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MH
MH
MH
MH
MH
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MH
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MH
MH
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MH
MH
MH
MH
-
Animals
Anoxia
Cell Proliferation
Cell Transformation,
Neoplastic
Computer Simulation
Humans
Imaging, ThreeDimensional
Models, Biological
Models, Molecular
Neoplasms/*blood
supply/*pathology
*Neovascularization,
Pathologic
Oxygen/chemistry
Software
Spheroids, Cellular
Time Factors
MH
-
Cell Proliferation
*Computer Simulation
Humans
*Models, Biological
Neoplasm Invasiveness
Neoplasms/*blood
supply/*pathology
- Time Factors
*Action Potentials
Animals
Calcium/metabolism
Calcium
Channels/physiology
Carrier
Proteins/physiology
Guinea Pigs
Heart/*physiology
Ion Channels/*physiology
Models, Biological
Potassium
Channels/physiology
Sodium-Calcium Exchanger
Sodium-PotassiumExchanging ATPase
Annotations for typical high throughput screens
3/16/2011
Google with "BIOMD:0000000201 BIOMODELS" returns one link, the correct one to the biomodels
DB.
Google with "GO:0007219 biomodels" tags from within the SBML file doesn't find the Biomodels file
at the BioModelsDB but does find a pdf version of the model at CalTech. (Three links total returned)
Google with "GO:0016055 PRO:000017443 HERBS AND JIMS BIG DATA AND COMPUTATIONAL
MODEL REPOSITORY" find the somitogenesis files in HERBS/JIMS but not the original or reannotated SBML file. (Google hasn't indexed it yet?)
3/23/2011
Still don't seem to find the biomodel files. Used the Biomodels DB tool to create a PDF summary
description of the model file (BIOMD0000000201.pdf) and added it to the repository.
Current file list on server:
model_repo_v0 - Revision 209:
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.3D_multi-cell_simulation_of_tumor_growth_and_angiogenesis.html.swp
.3D_multi-cell_simulation_of_tumor_growth_and_angiogenesis.html.swx
.DS_Store
.TemporaryItems/
0_Read_me.html
3D_multi-cell_simulation_of_tumor_growth_and_angiogenesis.html
3D_multi-cell_simulation_of_tumor_growth_and_angiogenesis.txt
BIOMD0000000201.pdf
BIOMD0000000201.xml
BIOMD0000000201_mod.xml
Crawling_Neutrophil_chasing_bacterium.mp4
Crawling_Neutrophil_chasing_bacterium_annot.wmv
Crawling_Neutrophil_chasing_bacterium_annotation.html
JimsStyle.css
Repository_notes.docx
Schoetz_cell_sorting/
document_list_IU.html
somitogenesis_CC3D_script.txt
somitogenesis_image.jpg
somitogenesis_image_CC3D_model.jpg
somitogenesis_image_CC3D_model_annotation.html
somitogenesis_image_annotation.html
4/5/2011
Checked again using "GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL
REPOSITORY" and "urn:miriam:obo.go:GO:0008543 HERBS AND JIMS BIG DATA AND
COMPUTATIONAL MODEL REPOSITORY", still not finding the original BioModels or the LaTex
versions of the BioModels file. Perhaps Google doesn't index terms such as
"urn:miriam:obo.go:GO:0008543"?
Added a table to the top of the BioModels pdf file with:
------------- added annotations jps -------------------------------HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY
Annotations added to a BioModels generated LaTex version of a BioModels SBML file.
urn:miriam:obo.go:GO%3A0007219
GO%3A0007219
urn:miriam:obo.go:GO%3A0008543
GO%3A0008543
urn:miriam:obo.go:GO%3A0016055
GO:0008543
GO:0016055
Notch signaling pathway
fibroblast growth factor receptor
signaling pathway
Wnt receptor signaling pathway
------------- end added annotations jps -------------------------------The new pdf file is BIOMD0000000201_mod.pdf
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Fixed misspelling of "biological" in several of the html file's keywords.
Gave the various HTML pages suitable HTML <title> tags.
4/7/2011
Google with:
"GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"Wnt receptor signaling pathway HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn:miriam:obo.go:GO%3A0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn:miriam:obo.go:GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn Miriam obo go GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn Miriam obo go GO 0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
No hits. Wait a couple more days and try again.
Multiple data sources should share a common biological description.
("C:\Users\James Sluka\Desktop\Biocomplexity\Ontologies\Common markup across multiple data source.pptx")
There is a newer version of the above figure (with an SBML model)
4/20/11
From Herbert:
James, sorry to take so long but I now have a url for you:
http://sys-bio.org/TestRepository/model_repo_v0.htm
This has a list of 10 biomodels in sbml and pdf format. To each sbml file I added this
text: "HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY Indiana University
Bloomington University of Washington"
Is there anything else I need to do?
Herb
Added his list of files to the index file (document_list_IU.html) and sent him a copy.
8/2/2011
FOAF annotations in RDF so Google will index
A FOAF file in RDF:
<?xml version="1.0"?>
<rdf:RDF xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<foaf:Person rdf:about="#JW">
<foaf:name>Jimmy Wales</foaf:name>
<foaf:mbox rdf:resource="mailto:jwales@bomis.com" />
<foaf:homepage rdf:resource="http://www.jimmywales.com/" />
<foaf:nick>Jimbo</foaf:nick>
<foaf:depiction rdf:resource="http://www.jimmywales.com/aus_img_small.jpg" />
<foaf:interest rdf:resource="http://www.wikimedia.org" rdfs:label="Wikipedia" />
<foaf:knows>
<foaf:Person>
<foaf:name>Angela Beesley</foaf:name>
</foaf:Person>
</foaf:knows>
</foaf:Person>
</rdf:RDF>
In RDF/XML
<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.semanticweb.org/owl/owlapi/turtle#"
xml:base="http://www.semanticweb.org/owl/owlapi/turtle"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
xmlns:p1="#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:daml="http://www.daml.org/2000/12/daml+oil#"
xmlns:oiled="http://oiled.man.example.net/test#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:ns0="http://cohse.semanticweb.org/ontologies/people#"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:map="http://www.gate.ac.uk/ns/ontologies/MappingMetamodel.owl#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#">
<!-///////////////////////////////////////////////////////////////////////////////////////
// Annotation properties
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-///////////////////////////////////////////////////////////////////////////////////////
// Individuals
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- #JW -->
<foaf:Person rdf:about="#JW">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<foaf:interest rdf:resource="http://www.wikimedia.org"/>
<foaf:homepage rdf:resource="http://www.jimmywales.com/"/>
<foaf:depiction rdf:resource="http://www.jimmywales.com/aus_img_small.jpg"/>
<foaf:mbox rdf:resource="mailto:jwales@bomis.com"/>
<foaf:knows>
<foaf:Person/>
</foaf:knows>
</foaf:Person>
<!-///////////////////////////////////////////////////////////////////////////////////////
// Annotations
///////////////////////////////////////////////////////////////////////////////////////
-->
<rdf:Description rdf:about="http://www.wikimedia.org">
<rdfs:label>Wikipedia</rdfs:label>
</rdf:Description>
</rdf:RDF>
<!-- Generated by the OWL API (version 3.2.1.1753) http://owlapi.sourceforge.net -->
RDF converters:
http://owl.cs.manchester.ac.uk/converter/convert
http://www.rdfabout.com/demo/validator/validate.xpd
My version using urn:Miriam:obo tags (GO:0008543 is FGFr signaling pathway). Not sure if the
GO:0008543 part should use something else for the ":". Not sure if the Miriam markup should be the
"about", the "name" or something else. Same with the "HERBS AND JIMS…"
<?xml version="1.0"?>
<rdf:RDF xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<foaf:Person rdf:about="#urn:miriam:obo.go:GO:0008543">
<foaf:name>fibroblast growth factor receptor signaling pathway</foaf:name>
<foaf:nick>FGFr signaling pathway</foaf:nick>
<foaf:knows>
<foaf:Person>
<foaf:name>HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY</foaf:name>
</foaf:Person>
</foaf:knows>
</foaf:Person>
</rdf:RDF>
Added to the top of the BIOMD0000000201_mod.xml file and saved as
BIOMD0000000201_mod_FOAF.xml.
8/8/2011
Added biomodel with the DBBR annotations in the <notes> block of the header.
BIOMD0000000201_DBBR_notes.xml
8/10/2011
Google q's for the BIOMD0000000201_DBBR_notes.xml:
urn:miriam:interpro:IPR013284 Distributed Biodata and Biomodel Resource
IPR013284 Distributed Biodata and Biomodel Resource
Beta-catenin Distributed Biodata and Biomodel Resource Distributed Biodata
and Biomodel Resource
No hits yet
Created Word and Excel versions of the raw XML BIOMD0000000201.xml file. Also created
versions of the DBBR annotated file.
BIOMD0000000201_DBBR_notes.xlsx
BIOMD0000000201.xlsx
BIOMD0000000201_DBBR_notes.docx
BIOMD0000000201.docx
8/15/2011
Still not found
8/22/2011
Google with query:
urn:miriam:interpro:IPR013284 Distributed Biodata and Biomodel Resource
Finds:
 BIOMD0000000201_DBBR_notes.xml - Cell Behavior Ontology
cellbehaviorontology.org/.../BIOMD0000000201_DBBR_notes.xml - Cached
Distributed Biodata and Biomodel Resource Annotations ... ERK1/2 MAP kinase ## DBBR: Bp
urn:miriam:interpro:IPR013284 Beta-catenin ## DBBR: Fgf ...
 [DOC]
BIOMD0000000201_DBBR_notes.docx - Cell Behavior Ontology
cellbehaviorontology.org/models/BIOMD0000000201_DBBR_notes.docx
Distributed Biodata and Biomodel Resource Annotations ######################## ..... <rdf:li
rdf:resource="urn:miriam:interpro:IPR013284"/> ...
 [XLS]
BIOMD0000000201_DBBR_notes.xlsx - Cell Behavior Ontology
cellbehaviorontology.org/models/BIOMD0000000201_DBBR_notes.xlsx
10, ########## Distributed Biodata and Biomodel Resource Annotations ..... 301, <rdf:li
rdf:resource="urn:miriam:interpro:IPR013284"/> ...
File name:
Q: urn:miriam:interpro:IPR013284 Distributed Biodata and Biomodel Resource
(IPR013284 is Beta-catenin) 4 hits total, first hit is the repository_notes.doc file.
BIOMD0000000201.docx
BIOMD0000000201.pdf
BIOMD0000000201.xlsx
BIOMD0000000201.xml
BIOMD0000000201_DBBR_notes.docx
BIOMD0000000201_DBBR_notes.xlsx
BIOMD0000000201_DBBR_notes.xml
BIOMD0000000201_mod.pdf
BIOMD0000000201_mod.xml
BIOMD0000000201_mod_FOAF.xml
Found by
Google?
no
no
no
no
Yes
Yes
Yes
no
no
no
Q: IPR013284 Distributed Biodata and Biomodel Resource
Finds the same three files
Q: Beta-catenin Distributed Biodata and Biomodel Resource
Finds the same three plus five non-DBBR files (relevant hits are all first)
Note that no files are found directly in the BioModels database!
5 April 2012: the sentence above no longer appears to be true. There are now static pages, e.g.,
http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth%2F2009-04
File: BIOMD0000000201_DBBR_notes.xml
<?xml version="1.0" encoding="UTF-8"?>
<!-- This model was downloaded from BioModels Database -->
<!-- Thu Mar 03 22:08:56 GMT 2011
-->
<!-- http://www.ebi.ac.uk/biomodels/
-->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" metaid="metaid_0000001" level="2" version="3">
<model metaid="metaid_0000002" id="Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF">
<notes>
########## Distributed Biodata and Biomodel Resource Annotations ########################
##
In this file
Ontology Term URN
Ontology Term
Synonyms
## DBBR: Rasi
urn:miriam:interpro:IPR001806
Small GTPase superfamily
## DBBR: D
urn:miriam:interpro:IPR003351
Dishevelled protein
## DBBR: N
urn:miriam:interpro:IPR008297
Notch
## DBBR: ERKa
urn:miriam:interpro:IPR008349
ERK1/2 MAP kinase
## DBBR: Bp
urn:miriam:interpro:IPR013284
Beta-catenin
## DBBR: Fgf
urn:miriam:interpro:IPR017338
Fibroblast growth factor, 15/19/21
## DBBR: MF
urn:miriam:interpro:IPR017374
Fringe
## DBBR: Bp
urn:miriam:kegg.compound:C00562
Phosphoprotein
## DBBR:
urn:miriam:kegg.pathway:ko04330
Notch signaling pathway
## DBBR: Rasa
urn:miriam:obo.chebi:CHEBI%3A15996
GTP
Guanosine 5'-triphosphate
## DBBR: Rasi
urn:miriam:obo.chebi:CHEBI%3A17552
GDP
Guanosine 5'-diphosphate, Guanosine diphosphate
## DBBR:
urn:miriam:obo.chebi:CHEBI%3A33699
messenger RNA
## DBBR:
urn:miriam:obo.go:GO%3A0001756
somitogenesis
formation of mesodermal clusters
## DBBR: cytosol
urn:miriam:obo.go:GO%3A0005829
cytosol
## DBBR:
urn:miriam:obo.go:GO%3A0006402
mRNA catabolic process
mRNA breakdown, mRNA catabolism, mRNA degradation
## DBBR:
urn:miriam:obo.go:GO%3A0006412
translation
protein biosynthesis, protein formation
## DBBR:
urn:miriam:obo.go:GO%3A0006468
protein phosphorylation
protein amino acid phosphorylation
## DBBR:
urn:miriam:reactome:REACT_11045.1
Pathway: Signaling by Wnt (Homo sapiens)
## DBBR:
urn:miriam:reactome:REACT_11065.1
Pathway: Beta-catenin phosphorylation cascade (Homo sapiens)
## DBBR:
urn:miriam:reactome:REACT_1482.4
Pathway: ERK activation (Homo sapiens)
## DBBR:
urn:miriam:reactome:REACT_299.2
Pathway: Signaling by Notch (Homo sapiens)
## DBBR:
urn:miriam:reactome:REACT_9470.2
Pathway: Signaling by FGFR (Homo sapiens)
## DBBR:
urn:miriam:taxonomy:32524
Amniota
amniotes
## DBBR: D
urn:miriam:uniprot:O14640
DVL1
Segment polarity protein dishevelled homolog DVL-1
Dishevelled-1, DSH homolog 1
## DBBR: Bp
urn:miriam:uniprot:P35222
Catenin beta-1
Beta-catenin, CTNNB1, CTNNB
## DBBR: N
urn:miriam:uniprot:P46531
Notch 1
Neurogenic locus notch homolog protein 1, hN1, Translocation-associated notch protein TAN1, Notch1, Tan1
## DBBR: K
urn:miriam:uniprot:P49841
GSK-3 beta
Glycogen synthase kinase-3 beta, GSK3B
## DBBR: MDusp
urn:miriam:uniprot:Q16828
DUSP6
Dual specificity protein phosphatase 6, Dual specificity protein phosphatase PYST1,
Mitogen-activated protein kinase phosphatase 3, MKP3, PYST1
## DBBR: MF
urn:miriam:uniprot:Q8NES3
LFNG
Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe, O-fucosylpeptide 3-beta-Nacetylglucosaminyltransferase
## DBBR: A
urn:miriam:uniprot:Q9Y2T1
AXIN2
Axin-2, Axin-like protein, Axil, Axis inhibition protein 2, Conductin
<p xmlns="http://www.w3.org/1999/xhtml">This is a model of the coupled Natch, Wnt and FGF modules as described in:<br/>
<b>A. Goldbeter and O. Pourqui�</b>,
<em>Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways.</em> J Theor Biol. 2008 Jun 7;252(3):574-85, pubmed ID:
<a href="http://www.ncbi.nlm.nih.gov/pubmed/18308339">18308339</a>
<br/>
To uncouple the modules remove the reaction
<em>MAx_trans_Xa</em> and set
<em>vsFK=vsF</em>.
<br/>
The SBML version of the model was converted from the CellML
<a href="http://www.cellml.org/models/goldbeter_pourquie_2008_version02">version</a> by Catherine Lloyd for the
<a href="http://www.cellml.org/models"> CellML repository </a>.
</p>
<p xmlns="http://www.w3.org/1999/xhtml">This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c)
2005-2010 The BioModels.net Team.<br/>
For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>.<br/>
To cite BioModels Database, please use: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20587024" target="_blank">Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E,
Henry A, Stefan MI, Snoep JL, Hucka M, Le Nov�re N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol.,
4:92.</a></p>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_0000002">
<dc:creator rdf:parseType="Resource">
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Lloyd</vCard:Family>
<vCard:Given>Catherine</vCard:Given>
Test to see if Google indexes Mathematica and MatLab files. File BIOMD0000000201.xml converted
to Mathematica (BIOMD0000000201_jasrnacLite2_2_mathematica.m) and MatLab
(BIOMD0000000201_jasrnacLite2_2_matlab.m) using JarnacLite2.
Added DBBR annotations from BIOMD0000000201_DBBR_notes.xml
BIOMD0000000201_jasrnacLite2_2_mathematica_DBBR_notes.m (In the "Synopsis" section.)
BIOMD0000000201_jasrnacLite2_2_matlab_DBBR_notes.m (% comments in the "Synopsis"
section.)
9/9/2011
Google with query: (same as last time I searched)
urn:miriam:interpro:IPR013284 Distributed Biodata and Biomodel Resource
Found the same 4 files (one is the word doc) as before
Google query for the somitogenesis files (using the old tag for DBBR) :
FMA:82840 embryonic cell GO:0016055 Wnt receptor signaling pathway HERBS AND
JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY
Finds just four files, all in the IU model repository (http://cbo.biocomplexity.indiana.edu/):
/models/somitogenesis_CC3D_script.txt
/svn/model_repo_v0/Repository_notes.docx
/svn/model_repo_v0/somitogenesis_image_CC3D_model_annotation.html
/svn/model_repo_v0/somitogenesis_image_annotation.html
(There are two paths to the same directory, http://cbo.biocomplexity.indiana.edu/models/ and
http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/ )
FOAF test. Looking for the FOAF annotated file BIOMD0000000201_mod_FOAF.xml
Google query:
HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY urn:miriam:obo.go:GO:0008543
Finds the word index doc and BIOMD0000000201_mod-2.pdf but not the FOAF marked file. Not
sure if FOAF just doesn't work or if it is a syntax problem and the xmlns:foaf tag isn't working right.
Biomodels style file (local) PDF version test, looking for BIOMD0000000201.pdf.
Google query (terms selected from "Table 3: Properties of each species.":
nuclear beta-catenin Notch protein Dusp6
Finds 29,700 hits
http://www.ebi.ac.uk/biomodels-main/BIOMD0000000201 (first non-"scholarly article" hit)
http://cytosolve.mit.edu/remote-model.php?model=../Models/Public/BioModels/BIOMD0000000201.xml
(2nd hit, page has a "species" table extracted from the SBML file)
http://antimony.sourceforge.net/examples/biomodels/BIOMD0000000201.txt (4th hit,
Jarnac type fie from the origianl SBML)
BIOMD0000000201_DBBR_notes.xml (7th hit)
BIOMD0000000201_DBBR_notes.docx (8th hit)
So, it doesn’t find the Biomodel in the Biomodel repository but does find a couple reformatted
versions (one in Jarnac and a page with the extracted table of included species).
A "light-weight" annotation block
Include URN to naming resources, include the name in the file being annotated, include any
available aliases and AKAs, include DBBR tag line
########## Distributed Biodata and Biomodel Resource Annotations ########################
##
In this file
Ontology Term URN
Ontology Term
## DBBR: Rasi
urn:miriam:interpro:IPR001806
Small GTPase superfamily
## DBBR: D
urn:miriam:interpro:IPR003351
Dishevelled protein
## DBBR: N
urn:miriam:interpro:IPR008297
Notch
## DBBR: ERKa
urn:miriam:interpro:IPR008349
ERK1/2 MAP kinase
## DBBR: Bp
urn:miriam:interpro:IPR013284
Beta-catenin
## DBBR: Fgf
urn:miriam:interpro:IPR017338
Fibroblast growth factor, 15/19/21
## DBBR: MF
urn:miriam:interpro:IPR017374
Fringe
## DBBR: Bp
urn:miriam:kegg.compound:C00562
Phosphoprotein
## DBBR:
urn:miriam:kegg.pathway:ko04330
Notch signaling pathway
## DBBR: Rasa
urn:miriam:obo.chebi:CHEBI%3A15996
GTP
## DBBR: Rasi
urn:miriam:obo.chebi:CHEBI%3A17552
GDP
## DBBR:
urn:miriam:obo.chebi:CHEBI%3A33699
messenger RNA
## DBBR:
urn:miriam:obo.go:GO%3A0001756
somitogenesis
## DBBR: cytosol
urn:miriam:obo.go:GO%3A0005829
cytosol
Synonyms
Guanosine 5'-triphosphate
Guanosine 5'-diphosphate
formation of mesodermal clusters
Columns are tab delimited. Within a column individual entries are comma delimited. Multiword
entries are not quoted but imbedded commas need to be escaped. If a given entity or concept has
multiple urns then each gets its own line in the table?
Colum
n
Contents
1
2
File type specific comment
Label/tag for this entity in this file
3
Ontology terms as a urn
4
5
Ontology term official name
Pseudonym list
Style
Notes
e.g. ## DBBR:
text
urn
text
text list
Often end is a numeric, e.g.,
urn:miriam:obo.chebi:CHEBI%3A15996
single name
list of names
4/2/2012
Added three files as test classes for OWL ontologies:
http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/pizz_jps_embed_edited_xml_in_comment.owl
http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/pizz_jps_manchester.owl
http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/pizz_jps.owl
The pizz_jps_embed_edited_xml_in_comment.owl file has the entire xml file "de-xml-ed" then
embedded into a comment tag.
The server appears to be MIA, sent Alin an email about it. Fixed.
TO DO: Check if Google indexes any of these ontology files.
11/9/2012
Added an annotated CC3D Python script:
angio_growth_steppables_08052009_01_45_36__CBOannotated.py
# CBO CBO_Object SystemQuality ComputationalPlatform Compucell3D
# CBO CBO_Process CellProcess CellGrowth
class VolumeParamSteppable(SteppablePy):
...
# CBO CBO_Process CellProcess CellDeath Necrosis
# GO:0008219 cell death
#Necrotic Cells
if cell.type == 3:
#set growth rate equation
cell.targetVolume-=0.5
cell.lambdaSurface=0