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‎.github/ISSUE_TEMPLATE/new-ontology.yml

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required: false
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- label: My term labels are in English and conform to the OBO Foundry [Naming Conventions](http://obofoundry.org/http://obofoundry.org/principles/fp-012-naming-conventions.html)
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required: false
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- label: I understand that term definitions, while not mandatory, are key to understanding the intentions of a term especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology have definitions, in English, using the [IAO:0000115](https://ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000115) property.
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- label: I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the [IAO:0000115](https://ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000115) property.
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required: false
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- label: For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
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required: false

‎_config.yml

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user: http://www.neuinfo.org
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- activity_status: active
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contact:
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email: jiezheng@pennmedicine.upenn.edu
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github: zhengj2007
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label: Jie Zheng
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orcid: 0000-0002-2999-0103
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email: jmwhorton@uams.edu
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github: jmwhorton
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label: Justin Whorton
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orcid: 0009-0003-4268-6207
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description: An ontology built for annotation and modeling of biobank repository
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and biobanking administration
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domain: investigations

‎docs/OntologyStatus.md

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Info: this page is non-normative; definitions may change.
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An ontology can be active, inactive, orphaned or obsolete
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(an additional status, "unresponsive", has been proposed but not yet ratified).
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These statuses depend on "Maintenance" (defined in [Principle 16](https://obofoundry.org/principles/fp-016-maintenance.html
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)) and "Responsiveness" ([Principle 20](https://obofoundry.org/principles/fp-016-maintenance.html)).
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The table below shows the statuses with their corresponding values for "Responsive" and "Maintained".
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|Status|Responsive|Maintained|
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|-----|--------|--------|
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|Active|yes|yes|
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|Inactive|yes|no|
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|Unresponsive (proposed)|no|yes|
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|Orphaned|no|no|
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"Obsolete" is a special status that is defined by the ontology representative rather than by OBO Foundry. It is like a confirmed version of "orphaned".
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- _active_: The ontology project has a contact person who is responsive. Terms, with resolvable IRIs, are being added (if the ontology is growing and not deemed complete) or other revisions made in response to community requests and/or the aims of the editorial team.
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- _inactive_: The ontology project has a contact person who is responsive. A version of the ontology is available, but no edits are being made and requests for edits are either greatly delayed or not being addressed by the ontology's editors.
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- _unresponsive_ (proposed): The ontology project does not have a contact person who is responsive, but the ontology is still being actively maintained.
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- _orphaned_: The ontology project does not have a contact person who is responsive. A static version of the ontology exists, but no edits are being made and requests for edits are not being addressed or responded to by the ontology's editors.
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- _obsolete_: The ontology is either inactive or orphaned, and the original developers do not recommend using existing versions of it, either because another project is available that supersedes it, or because previous produced versions have serious issues that make them less usable, and/or are not available at all.
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Please refer to the OBOFoundry GitHub [issue](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1126) for discussions on the subject.
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Please refer to the OBOFoundry GitHub [issue](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1126) and [other issue about "unresponsive"](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2255) for discussions on the subject.

‎ontology/eupath.md

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id: eupath
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title: VEuPathDB ontology
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contact:
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email: jiezheng@pennmedicine.upenn.edu
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email: jiezhen@med.umich.edu
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github: zhengj2007
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label: Jie Zheng
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orcid: 0000-0002-2999-0103
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- description: The VEuPathDB ontology is used in the MicrobiomeDB, a systems biology platform for integrating, mining and analyzing microbiome experiments.
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type: annotation and query
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user: https://microbiomedb.org
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activity_status: active
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activity_status: inactive
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---
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The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.

‎ontology/iao.md

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method: owl2obo
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source_url: http://purl.obolibrary.org/obo/iao.owl
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contact:
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email: jiezheng@pennmedicine.upenn.edu
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email: zhengj2007@gmail.com
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github: zhengj2007
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label: Jie Zheng
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orcid: 0000-0002-2999-0103

‎ontology/opl.md

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id: opl
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title: Ontology for Parasite LifeCycle
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contact:
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email: jiezheng@pennmedicine.upenn.edu
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email: zhengj2007@gmail.com
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github: zhengj2007
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label: Jie Zheng
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orcid: 0000-0002-2999-0103

‎registry/ontologies.jsonld

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{
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"activity_status": "active",
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"contact": {
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"email": "jiezheng@pennmedicine.upenn.edu",
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"github": "zhengj2007",
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"label": "Jie Zheng",
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"orcid": "0000-0002-2999-0103"
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"email": "jmwhorton@uams.edu",
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"github": "jmwhorton",
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"label": "Justin Whorton",
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"orcid": "0009-0003-4268-6207"
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},
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"description": "An ontology built for annotation and modeling of biobank repository and biobanking administration",
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"domain": "investigations",

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