From f251ea8ec0fd3b3ae74e272dfbe925de37a57d85 Mon Sep 17 00:00:00 2001 From: "Darren A. Natale" Date: Thu, 30 Nov 2023 09:13:45 -0500 Subject: [PATCH 1/3] Update new-ontology.yml instructions to better conform to principle 6 (#2475) In order to promote the importance of term descriptions, the instructions have been revised to remove the clause "while not necessary". At the same time, the necessity of descriptions for top-level terms is now emphasized. These changes bring the new ontology request form in better alignment with principle 6. --- .github/ISSUE_TEMPLATE/new-ontology.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/new-ontology.yml b/.github/ISSUE_TEMPLATE/new-ontology.yml index 8edf9bac2..8479f2dd8 100644 --- a/.github/ISSUE_TEMPLATE/new-ontology.yml +++ b/.github/ISSUE_TEMPLATE/new-ontology.yml @@ -268,7 +268,7 @@ body: required: false - 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) required: false - - 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. + - 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. required: false - 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). required: false From 564a90bdbdd7659e9972d39a9ee9bea704fb6def Mon Sep 17 00:00:00 2001 From: jie zheng Date: Thu, 7 Dec 2023 04:11:13 -0500 Subject: [PATCH 2/3] Update eupath.md (#2480) Updated contact person email and set the ontology to inactive Co-authored-by: Deepak --- ontology/eupath.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ontology/eupath.md b/ontology/eupath.md index 2cb804da2..9c239c648 100644 --- a/ontology/eupath.md +++ b/ontology/eupath.md @@ -3,7 +3,7 @@ layout: ontology_detail id: eupath title: VEuPathDB ontology contact: - email: jiezheng@pennmedicine.upenn.edu + email: jiezhen@med.umich.edu github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 @@ -37,7 +37,7 @@ usages: - description: The VEuPathDB ontology is used in the MicrobiomeDB, a systems biology platform for integrating, mining and analyzing microbiome experiments. type: annotation and query user: https://microbiomedb.org -activity_status: active +activity_status: inactive --- 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. From e080abfee6267f603e57ef5987170122dce52727 Mon Sep 17 00:00:00 2001 From: jie zheng Date: Thu, 7 Dec 2023 04:18:24 -0500 Subject: [PATCH 3/3] Update iao.md (#2481) update contact email Co-authored-by: Deepak --- ontology/iao.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/iao.md b/ontology/iao.md index c795e3607..5b94f29fc 100644 --- a/ontology/iao.md +++ b/ontology/iao.md @@ -6,7 +6,7 @@ build: method: owl2obo source_url: http://purl.obolibrary.org/obo/iao.owl contact: - email: jiezheng@pennmedicine.upenn.edu + email: zhengj2007@gmail.com github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103