All NIAID labels will be added as a GSCID-BRC alternative label. We may keep it in a separate OWL file
that can be imported based on user’s needs.
CP and CS refer to ‘Core Project’ and ‘Core Sample’ fields from the core metadata data dictionary
developed by the NIAID Metadata Working group Version 1.1. CP17 – CP 21 are required fields for
submissions to NCBI BioProject records. Please keep in mind that NCBI does not use an ontology. You
might notice that the examples they provide are mixture of different entity types. We propose creating
plan specification, as part of a study design, to cover these fields and allow us to group the
investigations based on the different aspects defined by NCBI. By reviewing the NCBI definitions and
examples, we believe that these fields specify different aspects of the main processes performed in an
investigation. The main processes of an investigation include (in order):
specimen collection -> purification of target material in the specimen -> sample preparation for assay
(target capture = evaluant of an assay) -> assay -> data analysis
The following CP20, CP17, CP21, CP18, CP19 order reflects the order of these processes performed in
the investigation.
The following is an example use case: ‘transcription profiling of parasite isolates collected from Lake
Ontario using RNA-seq assay’.
CP 20: what is the input of the specimen collection?
A portion of Lake Ontario. So it fits NCBIs ‘environment’ or ‘environmental material’
(http://purl.obolibrary.org/obo/ENVO_00010483) in OBI
CP 17: what is the target material in the specimen to be extracted?
The intent of the study is transcription profiling of collected isolates. Therefore, the target material in
the specimen is population of expressed transcripts based on RNA extracted from the specimen. So, it
fits NCBI’s ‘Transcriptome’ category.
CP 21: what is the target captured in the assay (and associated preparation needed for the assay)?
Transcription profiling can be accomplished by sequencing the whole RNA extract. So, it will fall in
‘Whole’ category.
CP 18: what assay is performed?
An RNA-seq assay will be done so it fits NCBI’s ‘Sequence’.
CP 19: what data generated is to be submitted?
We would like to submit the sequence reads generated directly from the RNA-seq assay without further
analysis. It falls in NCBI’s ‘raw sequence’ category.
Note: The terms we have requested so far are mapped to fields (categories) in the submission form. We
are planning to add the terms used in annotations into OBI in the future, such as, multi-species scope
specification as subclass of ‘specimen-based scope specification’.
OBI: specimen-based scope of investigation specification
A plan specification which specifies the scope of an investigation based on the heterogeneity of
organisms or type of material that are the specified input of specimen collection.
‘is part of’ some ‘study design’
‘is about’ some (is_specified_input_of some ‘specimen collection’)
NIAID/NCBI label: Sample Scope (CP20)
NIAID/NCBI definition Indicates the scope and purity of the biological sample used for the project.
NIAID/NCBI examples: Monoisolate, Multiisolate, Multi-species, Environment, Synthetic, Other (specify)
OBI: target material in specimen specification
A plan specification which specifies the type of material that will be assayed in an investigation.
‘is part of’ some ‘study design’
‘is about’ some (extract and is_specified_output_of some
(extraction and has_specified_input some specimen))
NIAID/NCBI label: Target Material (CP17)
NIAID/NCBI definition: Indicates the type of material that is isolated from the sample for use in the
project.
NIAID/NCBI examples: Genome, Purified chromosome, Transcriptome, Phenotype, Proteome
OBI: target capture specification
A plan specification which specifies how the material enrichment procedure will influence the scale, or
type of material that will be assayed in the specimen.
‘is part of’ some ‘study design’
‘is about’ some (material and ‘is part of’ some specimen and
‘has role’ some (‘evaluant role’ and ‘is realized by’ some assay))
NIAID/NCBI label: Target Capture (CP21)
NIAID/NCBI definition: Indicates the scale, or type, of information that the project is designed to
generate from the sample material.
NIAID/NCBI examples: Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey
OBI: investigation assay specification
A plan specification which indicates the assay type used to obtain data.
‘is part of’ some ‘study design’
‘is about’ some assay
NIAID/NCBI label: Project Method (CP18)
NIAID/ NCBI definition: Indicate the general approach used to obtain data.
NIAID/NCBI examples: Sequence, Array, Mass Spectrometry, Other (specify)
OBI: specification of data to be generated in an investigation
An objective specification which indicates the type of data that will be generated and submitted to a
database
‘is part of’ some ‘study design’
‘is about’ some (‘data item’ and is_specified_output_of some (assay or ‘data transformation’))
NIAID/NCBI label: Project Objectives (CP19)
NIAID/NCBI definition: Indicates the project goals with respect to the type of data that will be generated
and submitted to an INSDC database.
NIAID/NCBI examples: Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation,
Epigenetic markers, expression, maps, phenotype
OBI: specimen provider principal investigator
A person who is a principal investigator and provides the specimen
'Homo sapiens' and ('has role' some 'principal investigator role')
and (supplies some specimen)
NIAID label: Sample Provider Principal Investigator (PI) Name (CP6)
NIAID definition: Name of the responsible investigator providing the sample set and metadata for the
sequencing project
OBI: organization of specimen provider principal investigator
An organization that is the affiliation of the principal investigator providing the specimens for the
investigation
organization and 'has organization member' some 'specimen provider principal investigator’
NIAID label: Sample Provider PI's Institution (CP7)
NIAID definition: Institutional affiliation of the responsible investigator providing the sample set and
metadata for the sequencing project.
OBI: email address of specimen provider principal investigator
An email address of the principal investigator providing the specimens for the investigation
'email address' and 'is about' some ‘specimen provider principal investigator’
NIAID label: Sample Provider PI's email (CP8)
NIAID definition: Preferred email address of the responsible investigator providing the sample set and
metadata for the sequencing project
OBI currently only has ‘DNA sequencing service’. ‘sequencing service’ is required for following terms to
cover (direct) RNA and protein sequencing.
OBI: sequencing facility organization
An organization that provides sequence determination services
organization and ('has role' some ('service provider role'
and 'is realized by' some ‘sequencing service'))
NIAID label: Sequencing Facility (CP9)
NIAID definition: Name of the facility responsible for sequence determination; in many cases this will be
one of the DMID-supported Genome Sequence Centers for Infectious Diseases (GSCIDs)
OBI: sequencing facility contact person
A person who is the contact representative at the sequencing facility
'Homo sapiens' and ('has role' some 'contact representative role')
and ('is member of organization' some ’sequencing facility organization’)
NIAID label: Sequencing Facility Contact Name (CP10)
NIAID definition: Name of the responsible investigator leading the sequencing project at the sequencing
facility
OBI: organization of sequencing facility contact person
An organization that is the affiliation of the contact representative at the sequencing facility
organization and 'has organization member' some ‘sequencing facility contact person’
NIAID label: Sequencing Facility Contact's Institution (CP11)
NIAID definition: Institutional affiliation of the responsible investigator leading the sequencing project at
the sequencing facility
OBI: email address of sequencing facility contact person
An email address of the contact representative at the sequencing facility
'email address' and 'is about' some ‘sequencing facility contact person’
NIAID label: Sequencing Facility Contact's email (CP12)
NIAID definition: Preferred email address of the responsible investigator leading the sequencing project
at the sequencing facility
OBI: Bioinformatics Resource Center contact person
A person who is the contact representative of a Bioinformatics Resource Center
'Homo sapiens' and ('has role' some 'contact representative role')
and ('is member of organization' some 'Bioinformatics Resource Center')
NIAID label: Bioinformatics Resource Center Contact Name (CP14)
NIAID definition: Name of the responsible investigator leading the BRC responsible for managing the
data derived from the sequencing project
OBI: organization of Bioinformatics Resource Center contact person
An organization that is the affiliation of the person who is contact representative of a Bioinformatics
Resource Center
organization and
'has organization member' some ‘bioinformatics resource center contact person’
NIAID label: Bioinformatics Resource Center Contact's Institution (CP15)
NIAID definition: Institutional affiliation of the responsible investigator leading the BRC responsible for
managing the data derived from the sequencing project
OBI: email address of Bioinformatics Resource Center contact person
An email address of the person who is contact representative of a Bioinformatics Resource Center
'email address' and 'is about' some ‘bioinformatics resource center contact person’
NIAID label: Bioinformatics Resource Center Contact's email (CP16)
NIAID definition: Preferred email address of the responsible investigator leading the BRC responsible for
managing the data derived from the sequencing project
OBI: specimen repository organization
An organization that provides a service to store and distribute specimens
organization and ('has role' some ('service provider role'
and ('is realized by' some ('material storage service'
and has_specified_input some specimen))))
NIAID label: Specimen Repository (CS20)
NIAID definition: Name of repository where a specimen sample has been deposited.
OBI: specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
'specimen identifier'
and (is_specified_output_of some ('assigning a centrally registered identifier'
and 'has participant' some ‘specimen repository’))
NIAID label: Specimen Repository Sample ID (CS21)
NIAID definition: Unique identifier assigned by sample repository to identity the specimen sample.
OBI: specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
'specimen identifier'
and (is_specified_output_of some ('assigning a centrally registered identifier'
and 'has participant' some ‘sequencing facility organization’))
NIAID label: Sample ID - Sequencing Facility (CS22)
NIAID definition: Unique identifier used by the relevant sequencing center to identify the sample
submitted by the sample provider.
OBI: sample preparation for sequencing assay
Preparation of nucleic acids for a sequencing assay.
'sample preparation for assay'
and (has_specified_input some (specimen and 'has grain' some 'nucleic acid'))
and (has_specified_output some (specimen
and is_specified_input_of some 'sequencing assay'))
NIAID/NCBI label: Nucleic Acid Preparation Method (CS24)
NIAID/ NCBI definition: Details about the preparation of DNA samples for sequencing including if
amplification was used (e.g., in the case of sequencing a single mosquito), and any other relevant
molecular biology protocols done prior to sequencing.
OBI: comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting.
textual entity' and ('is about' some
('material entity' and ‘participates in’ some investigation
or 'planned process' and 'is part of' some investigation))
NIAID label: Comments (CS30)
NIAID definition: Any additional information about the initial specimen collection event, the sample
preparation process, the sequencing reaction, the data transformation steps, or any other aspect of the
project worth noting.
OBI: specimen collector
A person who collects the specimen
‘Homo sapiens’ and ‘has role’ some ‘specimen collector role’
NIAID label: Specimen Collector Name (CS31)
NIAID definition: Name of the person collecting the specimen and specimen collection metadata
OBI: organization of specimen collector
An organization that is the affiliation of the person collecting the specimen
organization and 'has organization member' some 'specimen collector’
NIAID label: Specimen Collector's Institution (CS32)
NIAID definition: Institutional affiliation of the person collecting the specimen and specimen collection
metadata
OBI: email address of specimen collector
An email address of the person collecting the specimen
‘email address' and 'is about' some 'specimen collector’
NIAID label: Specimen Collector's email (CS33)
NIAID definition: Preferred email address of the person collecting the specimen and specimen collection
metadata