pyobo/pyobo issues and pull requests

#168 - Improve Rhea import

Pull Request - State: open - Opened by cthoyt 10 months ago

#167 - Add participants to Rhea import

Issue - State: open - Opened by cmungall 10 months ago - 3 comments

#166 - Update synonym parsing to handle OMO CURIEs

Pull Request - State: closed - Opened by cthoyt 11 months ago

#165 - Annotate genes in FlyBase with SO terms

Issue - State: open - Opened by cthoyt 11 months ago

#164 - Use preferred prefixes when outputting OBO flat files

Pull Request - State: closed - Opened by cthoyt almost 1 year ago

#163 - Fix oboInOwl prefix

Pull Request - State: closed - Opened by matentzn about 1 year ago - 2 comments

#162 - Include overlaps relationship in interpro ingest

Issue - State: open - Opened by cmungall about 1 year ago

#161 - Use preferred prefixes when outputting OBO Format

Issue - State: closed - Opened by cmungall about 1 year ago

#160 - Various cleanup for large scale database generation

Pull Request - State: closed - Opened by cthoyt about 1 year ago

#159 - Enable specifying default prefix

Pull Request - State: open - Opened by cthoyt about 1 year ago

#158 - Fix pfam, rhea, and mirbase importers

Pull Request - State: closed - Opened by cthoyt about 1 year ago

#157 - New sources for funders

Issue - State: open - Opened by cthoyt about 1 year ago

#156 - Enforce all references are standardized

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

#155 - `pyobo.get_sssom_df()` for UMLS returns `prefix:PREFIX:ID`

Issue - State: closed - Opened by hrshdhgd over 1 year ago - 1 comment

#154 - Make adding names to SSSOM optional

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

#153 - Turn off name lookup in SSSOM export

Issue - State: closed - Opened by cthoyt over 1 year ago

#152 - Add pydantic1/2 compatibility

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

#151 - Update MeSH import for 2023+ data

Pull Request - State: closed - Opened by hrshdhgd over 1 year ago - 8 comments

#150 - Unidecode Error

Issue - State: closed - Opened by Crispae over 1 year ago - 8 comments

#149 - Update UniProt download

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

#148 - Unzipping resource file fails with EOFError

Issue - State: closed - Opened by kkaris over 1 year ago

#147 - Update sources

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

#146 - coordinate with SIB on conversion of EC

Issue - State: open - Opened by cmungall over 1 year ago

#145 - Improve support for default namespace when parsing OBO

Issue - State: open - Opened by cthoyt over 1 year ago

#144 - Errors related to robot conversion of vo

Issue - State: open - Opened by bgyori almost 2 years ago - 1 comment

#143 - Warning about NCIT version

Issue - State: closed - Opened by bgyori almost 2 years ago

#142 - Error processing EMAPA

Issue - State: closed - Opened by bgyori almost 2 years ago - 2 comments

#141 - Update sources

Pull Request - State: closed - Opened by cthoyt almost 2 years ago

#140 - coordinate with SIB on conversion of swisslipids

Issue - State: open - Opened by cmungall almost 2 years ago - 10 comments

#139 - FTP error when downloading PFAM

Issue - State: closed - Opened by cmungall almost 2 years ago - 4 comments

#138 - Update synonyms handling

Pull Request - State: closed - Opened by cthoyt almost 2 years ago

#137 - Enable specifying version for sources

Pull Request - State: closed - Opened by cthoyt almost 2 years ago

#136 - Issue when trying to retrieve a specific version of `HGNC`

Issue - State: closed - Opened by DimitrisAlivas about 2 years ago - 1 comment

#135 - Begin implementing obograph importer

Pull Request - State: open - Opened by cthoyt about 2 years ago

#134 - Upgrade python

Pull Request - State: closed - Opened by cthoyt about 2 years ago

#133 - Download fails on Anopheles gambiae

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

#132 - Update package configuration

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

#131 - Update version handling

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

#130 - Require static typing

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

#129 - Switch to class-based interface

Pull Request - State: closed - Opened by cthoyt about 3 years ago - 2 comments

#128 - Grab ICD-10 to ICD-11 mapping table

Issue - State: closed - Opened by cthoyt about 3 years ago - 1 comment

#127 - Externalize ontology loading from OBO clas

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

#126 - Get unavailable ontologies from OntoBee endpoint

Issue - State: open - Opened by cthoyt about 3 years ago

#125 - WHO Resources

Issue - State: open - Opened by cthoyt about 3 years ago

#124 - New source: BiGG Models Metabolite Database

Pull Request - State: open - Opened by samuelbunga about 3 years ago - 1 comment
Labels: Nomenclature Data

#123 - hgnc ingest fails with illegal prefix?

Issue - State: closed - Opened by matentzn about 3 years ago - 9 comments

#122 - Make sure identifiers in source column are normalized

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

#121 - Add Antibody Registry

Pull Request - State: closed - Opened by cthoyt about 3 years ago
Labels: Nomenclature Data

#120 - Enable passing a custom Gilda grounder class

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

#119 - How similar are model organism nomenclatures?

Issue - State: open - Opened by cthoyt about 3 years ago

#118 - Annotate genes in HGNC with SO terms

Issue - State: open - Opened by cthoyt about 3 years ago - 4 comments

#117 - Add descriptions to uniprot

Issue - State: open - Opened by cthoyt about 3 years ago

#116 - Fix interpro processing

Pull Request - State: closed - Opened by bgyori over 3 years ago - 1 comment

#115 - Interpro parsing issue

Issue - State: closed - Opened by bgyori over 3 years ago

#114 - Add selventa vocabularies

Pull Request - State: closed - Opened by cthoyt over 3 years ago
Labels: Nomenclature Data

#113 - Update Gilda code

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

#112 - Get list of identifiers

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

#111 - Add DepMap cell lines

Pull Request - State: closed - Opened by cthoyt over 3 years ago
Labels: Nomenclature Data

#110 - Add CCLE Cells

Pull Request - State: closed - Opened by cthoyt over 3 years ago
Labels: Nomenclature Data

#109 - Blacken code

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

#108 - Antibody registry

Issue - State: closed - Opened by cthoyt over 3 years ago
Labels: Nomenclature Data

#107 - Add signor names

Issue - State: open - Opened by cthoyt over 3 years ago
Labels: Nomenclature Data

#106 - SwissLipids

Issue - State: closed - Opened by cthoyt over 3 years ago
Labels: Nomenclature Data

#105 - Add UniProt vocabularies

Pull Request - State: closed - Opened by cthoyt over 3 years ago - 1 comment

#104 - Add uniprot names to ooh na na

Issue - State: closed - Opened by cthoyt over 3 years ago - 1 comment

#103 - UniProt subcellular locations

Issue - State: open - Opened by cthoyt over 3 years ago
Labels: Nomenclature Data

#102 - Enable usage of chembl database while zipped

Issue - State: closed - Opened by cthoyt over 3 years ago

#101 - Fix drugbank synonym loading

Issue - State: open - Opened by cthoyt over 3 years ago
Labels: bug

#100 - PTMsigDB

Issue - State: open - Opened by cthoyt over 3 years ago

#99 - Gene Ontology alternative identifiers don't make it to the database build

Issue - State: closed - Opened by cthoyt over 3 years ago
Labels: bug

#98 - Reorganize argument passing and docs

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

#97 - Refactor OBO Loading

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

#96 - Add darglint config

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

#95 - Add Rhea

Pull Request - State: closed - Opened by cthoyt almost 4 years ago

#94 - PharmGKB

Issue - State: open - Opened by cthoyt almost 4 years ago
Labels: Nomenclature Data

#93 - Fix synonym parsing

Pull Request - State: closed - Opened by cthoyt almost 4 years ago

#92 - ONCOTREE xrefs

Issue - State: open - Opened by cthoyt almost 4 years ago

#91 - Add license scan report and status

Pull Request - State: closed - Opened by fossabot almost 4 years ago - 1 comment

#90 - Get taxonomy mappings from MeSH 2021

Issue - State: closed - Opened by cthoyt almost 4 years ago - 1 comment
Labels: Xref Data

#89 - Issues with PubChem name/id mappings

Issue - State: open - Opened by bgyori about 4 years ago - 1 comment

#88 - Update PubChem version

Pull Request - State: closed - Opened by bgyori about 4 years ago - 3 comments

#87 - More chemistry

Issue - State: open - Opened by cthoyt about 4 years ago
Labels: Nomenclature Data

#86 - Add FamPlex

Pull Request - State: closed - Opened by cthoyt about 4 years ago

#85 - Make more careful relations to proteins and protein families

Pull Request - State: closed - Opened by cthoyt about 4 years ago

#84 - Get ICD10 and ICD11

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment
Labels: Nomenclature Data

#83 - Add drugbank salt support

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment
Labels: Nomenclature Data

#82 - Add plugins

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment

#81 - Fix broken DOID link

Pull Request - State: closed - Opened by ddomingof about 4 years ago

#80 - Handle salts in DrugBank

Issue - State: closed - Opened by bgyori about 4 years ago - 2 comments

#79 - Add GBIF

Issue - State: closed - Opened by cthoyt about 4 years ago
Labels: Nomenclature Data

#78 - Add structural information to ChEBML terms' xrefs

Issue - State: open - Opened by cthoyt about 4 years ago

#77 - Add mocks, tests, and 3.6 compatibility

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment

#76 - Implement lots of mocks and make unittests work on Travis

Issue - State: closed - Opened by cthoyt about 4 years ago

#75 - Automatically parse out ITIS version number

Pull Request - State: closed - Opened by cthoyt about 4 years ago

#74 - Fix get name lookup when there are no alts available

Pull Request - State: closed - Opened by cthoyt about 4 years ago

#73 - Implement getter for Wikidata exact mappings

Pull Request - State: closed - Opened by cthoyt about 4 years ago

#71 - Improve error messages when missing UMLS data

Issue - State: closed - Opened by ddomingof about 4 years ago - 1 comment

#69 - Update ITIS dump

Issue - State: closed - Opened by ddomingof about 4 years ago

#65 - Issues with ChEBML mappings

Issue - State: closed - Opened by bgyori over 4 years ago - 3 comments

#59 - Improve pattern curation and add regex checking to resolver

Issue - State: open - Opened by cthoyt over 4 years ago - 1 comment

GitHub / pyobo/pyobo issues and pull requests