Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / geneontology/neo issues and pull requests

#117 - Add FB Developmental and Anatomy Ontology

Issue - State: closed - Opened by hattrill 11 months ago - 11 comments

#117 - Add FB Developmental and Anatomy Ontology

Issue - State: closed - Opened by hattrill 11 months ago - 11 comments

#116 - add additional species names to gene labels

Issue - State: open - Opened by balhoff over 1 year ago - 5 comments

#116 - add additional species names to gene labels

Issue - State: open - Opened by balhoff over 1 year ago - 5 comments

#114 - Ecoli data is gone from NEO as the upstream source changed

Issue - State: open - Opened by kltm over 1 year ago - 13 comments
Labels: bug (B: affects usability)

#114 - Ecoli data is gone from NEO as the upstream source changed

Issue - State: open - Opened by kltm over 1 year ago - 13 comments
Labels: bug (B: affects usability)

#113 - Ensure AGI_LocusCode IDs are compacted in oio:id values.

Pull Request - State: closed - Opened by balhoff over 1 year ago - 1 comment

#112 - In some cases bad identifiers are getting into the load

Issue - State: open - Opened by kltm over 1 year ago - 5 comments

#112 - In some cases bad identifiers are getting into the load

Issue - State: open - Opened by kltm over 1 year ago - 5 comments

#111 - Some e.coli entries not found

Issue - State: open - Opened by pgaudet about 2 years ago - 18 comments

#111 - Some e.coli entries not found

Issue - State: open - Opened by pgaudet about 2 years ago - 18 comments

#109 - Xenbase identifiers are not correct getting labels (in NEO?)

Issue - State: closed - Opened by kltm about 2 years ago - 5 comments

#109 - Xenbase identifiers are not correct getting labels (in NEO?)

Issue - State: closed - Opened by kltm about 2 years ago - 5 comments

#108 - Fix ampersand in XML issue

Pull Request - State: closed - Opened by balhoff about 2 years ago - 1 comment

#108 - Fix ampersand in XML issue

Pull Request - State: closed - Opened by balhoff about 2 years ago - 1 comment

#107 - Add correct expansion for AGI_LocusCode prefix.

Pull Request - State: closed - Opened by balhoff about 2 years ago - 1 comment

#107 - Add correct expansion for AGI_LocusCode prefix.

Pull Request - State: closed - Opened by balhoff about 2 years ago - 1 comment

#106 - unresolved IDs

Issue - State: open - Opened by tmushayahama over 2 years ago - 10 comments

#106 - unresolved IDs

Issue - State: open - Opened by tmushayahama over 2 years ago - 10 comments

#105 - Get non-mouse PRO ids into Noctua for use in annotation

Issue - State: open - Opened by hdrabkin over 7 years ago - 11 comments
Labels: bug (B: affects usability)

#105 - Get non-mouse PRO ids into Noctua for use in annotation

Issue - State: open - Opened by hdrabkin over 7 years ago - 11 comments
Labels: bug (B: affects usability)

#104 - Transient Xenbase issue dropped GPI file

Issue - State: closed - Opened by malcolmfisher103 over 2 years ago - 1 comment

#104 - Transient Xenbase issue dropped GPI file

Issue - State: closed - Opened by malcolmfisher103 over 2 years ago - 1 comment

#103 - Some IDs we expect are not found in Noctua

Issue - State: closed - Opened by pgaudet over 2 years ago - 5 comments
Labels: bug

#103 - Some IDs we expect are not found in Noctua

Issue - State: closed - Opened by pgaudet over 2 years ago - 5 comments
Labels: bug

#102 - Isoform display in label (originally on the visual tool)

Issue - State: open - Opened by pmasson55 over 2 years ago - 4 comments

#102 - Isoform display in label (originally on the visual tool)

Issue - State: open - Opened by pmasson55 over 2 years ago - 4 comments

#101 - Use correct IRI form for RNAcentral.

Pull Request - State: closed - Opened by balhoff over 2 years ago

#101 - Use correct IRI form for RNAcentral.

Pull Request - State: closed - Opened by balhoff over 2 years ago

#100 - RNAcentral IDs incorrectly use OBO PURL namespace

Issue - State: closed - Opened by balhoff over 2 years ago - 5 comments

#100 - RNAcentral IDs incorrectly use OBO PURL namespace

Issue - State: closed - Opened by balhoff over 2 years ago - 5 comments

#99 - Clarify and implement rules on inclusion of RNA gene products / RNA central

Issue - State: open - Opened by cmungall over 2 years ago - 4 comments

#96 - Many ChEBI chemicals not available for metabolic models

Issue - State: open - Opened by marcfeuermann over 2 years ago - 17 comments

#96 - Many ChEBI chemicals not available for metabolic models

Issue - State: open - Opened by marcfeuermann over 2 years ago - 17 comments

#95 - Request to load more phage proteins

Issue - State: closed - Opened by dsiegele over 2 years ago - 2 comments
Labels: duplicate

#95 - Request to load more phage proteins

Issue - State: closed - Opened by dsiegele over 2 years ago - 2 comments
Labels: duplicate

#94 - Would like phage proteins to be available

Issue - State: closed - Opened by dsiegele over 2 years ago - 2 comments
Labels: enhancement

#94 - Would like phage proteins to be available

Issue - State: closed - Opened by dsiegele over 2 years ago - 2 comments
Labels: enhancement

#93 - Xenbase entities do not seem to propagate to the NEO build from the Xenbase GPI

Issue - State: closed - Opened by kltm over 2 years ago - 6 comments
Labels: bug

#93 - Xenbase entities do not seem to propagate to the NEO build from the Xenbase GPI

Issue - State: closed - Opened by kltm over 2 years ago - 6 comments
Labels: bug

#91 - Some Reactome Identifiers are not resolving

Issue - State: open - Opened by ukemi over 2 years ago - 11 comments
Labels: bug

#91 - Some Reactome Identifiers are not resolving

Issue - State: open - Opened by ukemi over 2 years ago - 11 comments
Labels: bug

#90 - Add minimal QC for NEO

Pull Request - State: open - Opened by kltm over 2 years ago

#90 - Add minimal QC for NEO

Pull Request - State: open - Opened by kltm over 2 years ago

#89 - Add some minimal QC to the NEO pipeline

Issue - State: open - Opened by kltm over 2 years ago - 14 comments
Labels: enhancement

#89 - Add some minimal QC to the NEO pipeline

Issue - State: open - Opened by kltm over 2 years ago - 14 comments
Labels: enhancement

#88 - Trace entities that do not create nice URIs (i.e. compact well to CURIEs in out pipeline) in NEO

Issue - State: closed - Opened by kltm over 2 years ago - 2 comments
Labels: question

#88 - Trace entities that do not create nice URIs (i.e. compact well to CURIEs in out pipeline) in NEO

Issue - State: closed - Opened by kltm over 2 years ago - 2 comments
Labels: question

#87 - Issue 82 add all reviewed

Pull Request - State: closed - Opened by kltm over 2 years ago

#86 - Hacks in the NEO build process prevent branches from coexisting

Issue - State: closed - Opened by kltm over 2 years ago - 1 comment
Labels: bug

#86 - Hacks in the NEO build process prevent branches from coexisting

Issue - State: closed - Opened by kltm over 2 years ago - 1 comment
Labels: bug

#85 - (Re)add sar-cov-2 GPI to NEO load

Issue - State: closed - Opened by kltm over 2 years ago - 3 comments

#85 - (Re)add sar-cov-2 GPI to NEO load

Issue - State: closed - Opened by kltm over 2 years ago - 3 comments

#84 - Use ROBOT instead of owltools in NEO build

Issue - State: open - Opened by kltm over 2 years ago - 1 comment

#84 - Use ROBOT instead of owltools in NEO build

Issue - State: open - Opened by kltm over 2 years ago - 1 comment

#83 - Use ROBOT instead of owltools.

Pull Request - State: open - Opened by balhoff over 2 years ago - 1 comment

#83 - Use ROBOT instead of owltools.

Pull Request - State: open - Opened by balhoff over 2 years ago - 1 comment

#82 - Load all Swiss-Prot entries in NEO

Issue - State: closed - Opened by pgaudet over 2 years ago - 22 comments

#82 - Load all Swiss-Prot entries in NEO

Issue - State: closed - Opened by pgaudet over 2 years ago - 22 comments

#81 - Ensure Complex Portal ids are correctly structured and typed

Pull Request - State: closed - Opened by balhoff over 2 years ago - 3 comments

#81 - Ensure Complex Portal ids are correctly structured and typed

Pull Request - State: closed - Opened by balhoff over 2 years ago - 3 comments

#79 - add reviewed viruses and bacteria, adjust script to add filer

Pull Request - State: closed - Opened by kltm over 2 years ago

#79 - add reviewed viruses and bacteria, adjust script to add filer

Pull Request - State: closed - Opened by kltm over 2 years ago

#78 - ChEBI : limit load to ChEBI that have 'UniProt' synonyms

Issue - State: open - Opened by pgaudet over 2 years ago - 10 comments
Labels: enhancement

#78 - ChEBI : limit load to ChEBI that have 'UniProt' synonyms

Issue - State: open - Opened by pgaudet over 2 years ago - 10 comments
Labels: enhancement

#77 - Include viruses and bacteria in NEO

Issue - State: closed - Opened by pgaudet over 2 years ago - 26 comments
Labels: enhancement

#77 - Include viruses and bacteria in NEO

Issue - State: closed - Opened by pgaudet over 2 years ago - 26 comments
Labels: enhancement

#76 - Include Human Protein complexes in NEO

Issue - State: closed - Opened by pgaudet over 2 years ago - 21 comments
Labels: enhancement

#76 - Include Human Protein complexes in NEO

Issue - State: closed - Opened by pgaudet over 2 years ago - 21 comments
Labels: enhancement

#75 - Include Alliance automated gene descriptions as 'definitions' for gene entries

Issue - State: open - Opened by vanaukenk almost 3 years ago - 3 comments
Labels: enhancement

#75 - Include Alliance automated gene descriptions as 'definitions' for gene entries

Issue - State: open - Opened by vanaukenk almost 3 years ago - 3 comments
Labels: enhancement

#74 - PRO ids map to more than one gene in PomBase gpi file - causing a neo build error

Issue - State: closed - Opened by vanaukenk about 3 years ago - 33 comments
Labels: PRO identifiers

#74 - PRO ids map to more than one gene in PomBase gpi file - causing a neo build error

Issue - State: closed - Opened by vanaukenk about 3 years ago - 33 comments
Labels: PRO identifiers

#73 - Model made in graph editor will not load into ART or Form

Issue - State: closed - Opened by hdrabkin about 3 years ago - 25 comments
Labels: bug, duplicate

#72 - Check type of mouse ncRNA genes - not recognized in Noctua as valid annotation objects

Issue - State: closed - Opened by vanaukenk about 3 years ago - 7 comments
Labels: bug

#72 - Check type of mouse ncRNA genes - not recognized in Noctua as valid annotation objects

Issue - State: closed - Opened by vanaukenk about 3 years ago - 7 comments
Labels: bug

#71 - Fix split limit bug; small env addition for testing

Pull Request - State: closed - Opened by kltm about 3 years ago - 3 comments

#71 - Fix split limit bug; small env addition for testing

Pull Request - State: closed - Opened by kltm about 3 years ago - 3 comments

#70 - MGI miRNA identifiers unavailable in NEO?

Issue - State: closed - Opened by vanaukenk over 3 years ago - 22 comments
Labels: bug, priority:1

#70 - MGI miRNA identifiers unavailable in NEO?

Issue - State: closed - Opened by vanaukenk over 3 years ago - 22 comments
Labels: bug, priority:1

#69 - NEO no longer building

Issue - State: closed - Opened by kltm over 3 years ago - 10 comments
Labels: bug

#69 - NEO no longer building

Issue - State: closed - Opened by kltm over 3 years ago - 10 comments
Labels: bug

#68 - Update Makefile with new location for sars-cov-2 data (kg)

Pull Request - State: closed - Opened by kltm over 3 years ago

#68 - Update Makefile with new location for sars-cov-2 data (kg)

Pull Request - State: closed - Opened by kltm over 3 years ago

#67 - Create test runner for GitHub Actions

Pull Request - State: closed - Opened by balhoff over 3 years ago - 5 comments

#67 - Create test runner for GitHub Actions

Pull Request - State: closed - Opened by balhoff over 3 years ago - 5 comments

#66 - Tweak obo-uris hack to handle hash injected by OBO parser

Issue - State: closed - Opened by kltm over 3 years ago - 1 comment
Labels: bug

#66 - Tweak obo-uris hack to handle hash injected by OBO parser

Issue - State: closed - Opened by kltm over 3 years ago - 1 comment
Labels: bug

#65 - Tweak obo-uris hack to handle hash injected by OBO parser.

Pull Request - State: closed - Opened by balhoff over 3 years ago - 12 comments

#65 - Tweak obo-uris hack to handle hash injected by OBO parser.

Pull Request - State: closed - Opened by balhoff over 3 years ago - 12 comments

#64 - Is NEO typing PRO identifiers correctly?

Issue - State: closed - Opened by vanaukenk over 3 years ago - 5 comments
Labels: PRO identifiers

#63 - accept both gpi2 and gpi1 (untested)

Pull Request - State: closed - Opened by cmungall over 3 years ago - 3 comments

#63 - accept both gpi2 and gpi1 (untested)

Pull Request - State: closed - Opened by cmungall over 3 years ago - 3 comments

#62 - NEO no longer builds in the pipeline

Issue - State: closed - Opened by kltm almost 4 years ago - 15 comments
Labels: bug

#62 - NEO no longer builds in the pipeline

Issue - State: closed - Opened by kltm almost 4 years ago - 15 comments
Labels: bug

#61 - consider updating wormbase expansion

Issue - State: open - Opened by balhoff almost 4 years ago - 3 comments