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Ontology for Biomedical Investigations (OBI)
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
- 1: collection of specimens [OBI_0002076]
- 2: organism [OBI_0100026]
- 3: planned process [OBI_0000011]
- 4: population [OBI_0000181]
- 5: reagent role [OBI_0000086]
- 6: specimen [OBI_0100051]
- 7: specimen collection objective [OBI_0000684]
- 8: specimen collection process [OBI_0000659]
- 9: specimen role [OBI_0000112]
1 - collection of specimens [OBI_0002076]
A material entity that has two or more specimens as its parts.
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerOpen collection of specimens in VFB
Term Information
- ID: OBI_0002076
- Name: collection of specimens
- Definition: A material entity that has two or more specimens as its parts.
- Synonyms:
- Type:
- Comment:
VFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0002076",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0002076",
"unique_facets": [
"Class"
],
"label": "collection of specimens"
},
"description": [
"A material entity that has two or more specimens as its parts."
],
"comment": []
},
"query": "Get JSON for Class",
"version": "3b19da3",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/BFO_0000040",
"types": [
"Entity",
"Class",
"has_subClass"
],
"short_form": "BFO_0000040",
"unique_facets": [
"Class"
],
"label": "material entity"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"unique_facets": [
"pub"
],
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}
2 - organism [OBI_0100026]
Category=external. [object; organismal entity; organism]
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerVFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0100026",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0100026",
"label": "organism"
},
"description": [],
"comment": [
"Category=external."
]
},
"query": "Get JSON for Class",
"version": "44725ae",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/BFO_0000030",
"types": [
"Entity",
"Class"
],
"short_form": "BFO_0000030",
"label": "object"
},
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/GENO_0000904",
"types": [
"Entity",
"Class"
],
"short_form": "GENO_0000904",
"label": "organismal entity"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": []
}
3 - planned process [OBI_0000011]
A processual entity that realizes a plan which is the concretization of a plan specification.
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerVFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000011",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000011",
"label": "planned process"
},
"description": [
"A processual entity that realizes a plan which is the concretization of a plan specification."
],
"comment": []
},
"query": "Get JSON for Class",
"version": "44725ae",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/BFO_0000015",
"types": [
"Entity",
"Class"
],
"short_form": "BFO_0000015",
"label": "process"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}
4 - population [OBI_0000181]
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerVFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000181",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000181",
"label": "population"
},
"description": [
"a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area"
],
"comment": []
},
"query": "Get JSON for Class",
"version": "44725ae",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/GENO_0000113",
"types": [
"Entity",
"Class"
],
"short_form": "GENO_0000113",
"label": "taxonomic group"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}
5 - reagent role [OBI_0000086]
[reagent role]
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerVFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000086",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000086",
"label": "reagent role"
},
"description": [],
"comment": []
},
"query": "Get JSON for Class",
"version": "44725ae",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/BFO_0000023",
"types": [
"Entity",
"Class"
],
"short_form": "BFO_0000023",
"label": "role"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": []
}
6 - specimen [OBI_0100051]
A material entity that has the specimen role.
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerTerm Information
- ID: OBI_0100051
- Name: specimen
- Definition: A material entity that has the specimen role.
- Synonyms:
- Type:
- Comment:
VFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0100051",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0100051",
"unique_facets": [
"Class"
],
"label": "specimen"
},
"description": [
"A material entity that has the specimen role."
],
"comment": []
},
"query": "Get JSON for Class",
"version": "3b19da3",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/BFO_0000040",
"types": [
"Entity",
"Class",
"has_subClass"
],
"short_form": "BFO_0000040",
"unique_facets": [
"Class"
],
"label": "material entity"
}
],
"relationships": [
{
"relation": {
"iri": "http://purl.obolibrary.org/obo/RO_0000087",
"label": "has role",
"type": "has_role"
},
"object": {
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/OBI_0000112",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000112",
"unique_facets": [
"Class"
],
"label": "specimen role"
}
}
],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"unique_facets": [
"pub"
],
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}
7 - specimen collection objective [OBI_0000684]
A objective specification to obtain a material entity for potential use as an input during an investigation.
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerOpen specimen collection objective in VFB
Term Information
- ID: OBI_0000684
- Name: specimen collection objective
- Definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
- Synonyms:
- Type:
- Comment:
VFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000684",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000684",
"unique_facets": [
"Class"
],
"label": "specimen collection objective"
},
"description": [
"A objective specification to obtain a material entity for potential use as an input during an investigation."
],
"comment": []
},
"query": "Get JSON for Class",
"version": "3b19da3",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/IAO_0000005",
"types": [
"Entity",
"Class",
"has_subClass"
],
"short_form": "IAO_0000005",
"unique_facets": [
"Class"
],
"label": "IAO_0000005"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"unique_facets": [
"pub"
],
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}
8 - specimen collection process [OBI_0000659]
A planned process with the objective of collecting a specimen.
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerOpen specimen collection process in VFB
Term Information
- ID: OBI_0000659
- Name: specimen collection process
- Definition: A planned process with the objective of collecting a specimen.
- Synonyms:
- Type:
- Comment:
VFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000659",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000659",
"unique_facets": [
"Class"
],
"label": "specimen collection process"
},
"description": [
"A planned process with the objective of collecting a specimen."
],
"comment": []
},
"query": "Get JSON for Class",
"version": "3b19da3",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/OBI_0000011",
"types": [
"Entity",
"Class",
"has_subClass"
],
"short_form": "OBI_0000011",
"unique_facets": [
"Class"
],
"label": "planned process"
}
],
"relationships": [
{
"relation": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000299",
"label": "has_specified_output",
"type": "has_specified_output"
},
"object": {
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/OBI_0100051",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0100051",
"unique_facets": [
"Class"
],
"label": "specimen"
}
},
{
"relation": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000293",
"label": "has_specified_input",
"type": "has_specified_input"
},
"object": {
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/BFO_0000040",
"types": [
"Entity",
"Class",
"has_subClass"
],
"short_form": "BFO_0000040",
"unique_facets": [
"Class"
],
"label": "material entity"
}
},
{
"relation": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000417",
"label": "achieves_planned_objective",
"type": "achieves_planned_objective"
},
"object": {
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/OBI_0000684",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000684",
"unique_facets": [
"Class"
],
"label": "specimen collection objective"
}
}
],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"unique_facets": [
"pub"
],
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}
9 - specimen role [OBI_0000112]
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerTerm Information
- ID: OBI_0000112
- Name: specimen role
- Definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
- Synonyms:
- Type:
- Comment:
VFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/OBI_0000112",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "OBI_0000112",
"unique_facets": [
"Class"
],
"label": "specimen role"
},
"description": [
"a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"
],
"comment": []
},
"query": "Get JSON for Class",
"version": "3b19da3",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/BFO_0000023",
"types": [
"Entity",
"Class",
"has_subClass"
],
"short_form": "BFO_0000023",
"unique_facets": [
"Class"
],
"label": "role"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"unique_facets": [
"pub"
],
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}