Ecosyste.ms: Issues

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

GitHub / bio4j/bio4j issues and pull requests

#168 - Add description properties to Enzyme classes

Issue - State: open - Opened by eparejatobes almost 8 years ago
Labels: feature, module: enzymedb

#167 - NULL should not be a UniProt keyword

Pull Request - State: closed - Opened by eparejatobes almost 8 years ago - 1 comment

#166 - Fixed Codacy badge link

Pull Request - State: closed - Opened by laughedelic about 8 years ago - 1 comment

#165 - Minor NCBITaxonomy model improvements

Pull Request - State: closed - Opened by laughedelic about 8 years ago - 4 comments
Labels: enhancement

#164 - Update to angulillos 0.9.1

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#163 - Update build configuration

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#162 - UniProt keyword categories should include "null"

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: bug, module: uniprot

#161 - Add generic tests

Issue - State: open - Opened by eparejatobes about 8 years ago
Labels: feature, module: go, module: uniprot, module: ncbi-taxonomy, module: enzymedb, module: uniref

#160 - Review Enzyme types

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: enhancement, module: enzymedb

#159 - Review NCBI Taxonomy graph

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 9 comments
Labels: docs, enhancement, module: ncbi-taxonomy

#158 - generate and review docs

Pull Request - State: open - Opened by eparejatobes about 8 years ago - 1 comment
Labels: 2 - in progress

#157 - UniProt Enzyme annotations

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 2 comments

#156 - Add Enzyme classes

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#155 - Remove has_part from GO

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#154 - GO UniProt cross-reference

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 2 comments
Labels: feature, module: go, module: uniprot

#153 - Review UniProt citation/references/evidence model

Issue - State: open - Opened by eparejatobes about 8 years ago
Labels: docs, enhancement, 1 - planned

#152 - Add UniProt protein NCBI taxonomy annotations

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: feature, module: uniprot, module: ncbi-taxonomy

#151 - Generate docs

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#150 - Refactor UniRef model

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 2 comments
Labels: module: uniref

#149 - Gene locations

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 2 comments
Labels: feature, module: uniprot

#148 - Declare vertices first, then edges

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 3 comments

#147 - add an index on keyword type id

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: feature

#146 - Update documentation for geneProducts edge

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 2 comments
Labels: docs

#145 - Remove isCanonical from proteins

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: docs, enhancement, module: uniprot

#144 - Add protein sequence length

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: docs, feature, module: uniprot

#143 - Add accession to canonical proteins

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: docs, feature, module: uniprot

#142 - Rename protein accession to ID

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: docs, bug, module: uniprot

#141 - Add description to Protein annotations

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#140 - Add a name property to genes

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment
Labels: module: uniprot

#139 - Add a Comments edge to Proteins

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#138 - Fix project definition - Java project

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 1 comment

#137 - Update build infrastructure

Pull Request - State: closed - Opened by eparejatobes about 8 years ago - 2 comments

#136 - Document UniProt graph

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 2 comments

#135 - Update UniProt - GO graph

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 1 comment

#134 - no need for separate packages

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 2 comments

#133 - Review UniProt graph

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 1 comment
Labels: docs, module: uniprot

#132 - Review Enzyme graph

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 5 comments

#131 - move import code to a separate repo

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 3 comments
Labels: enhancement, import

#130 - Set up pullapprove

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 1 comment
Labels: enhancement

#129 - Generic code for database cross-references

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 7 comments
Labels: feature, 3 - needs review

#128 - Deprecate UniProt keywords

Pull Request - State: closed - Opened by eparejatobes over 8 years ago
Labels: docs, meeting, module: uniprot

#127 - Review UniProt sequence annotations (features)

Issue - State: closed - Opened by eparejatobes over 8 years ago - 4 comments
Labels: docs, enhancement, module: uniprot, question

#126 - Remove redundant methods in vertices and edges

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 1 comment
Labels: enhancement

#125 - Remove graph dependencies

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 2 comments
Labels: enhancement

#124 - Upgrade to angulillos 0.9.x

Pull Request - State: closed - Opened by laughedelic over 8 years ago - 9 comments

#123 - Depend only on jdom2

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 1 comment

#122 - Store all protein names in a property

Issue - State: closed - Opened by eparejatobes over 8 years ago
Labels: enhancement, module: uniprot

#121 - Deprecate UniProt taxonomy

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 1 comment
Labels: docs, module: uniprot, question

#120 - Review database cross-references

Issue - State: open - Opened by eparejatobes over 8 years ago - 4 comments
Labels: docs, enhancement, 3 - needs review, question, refactoring

#119 - Review Gene vertices

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 4 comments
Labels: docs, module: uniprot, refactoring

#118 - Refactor UniRef module code

Issue - State: closed - Opened by laughedelic over 8 years ago
Labels: refactoring, module: uniref

#117 - Refactor EnzymeDB module code

Issue - State: closed - Opened by laughedelic over 8 years ago - 1 comment
Labels: refactoring, module: enzymedb

#116 - Review GO graph

Pull Request - State: closed - Opened by laughedelic over 8 years ago - 4 comments
Labels: docs, module: go

#115 - Review NCBI Taxonomy graph

Pull Request - State: closed - Opened by laughedelic over 8 years ago - 8 comments
Labels: docs, module: ncbi-taxonomy

#114 - Add an enum for keyword type

Issue - State: closed - Opened by eparejatobes over 8 years ago

#113 - IntAct data: Long term plans and discussion

Issue - State: open - Opened by eparejatobes over 8 years ago
Labels: docs, module: uniprot, question

#112 - Review Protein vertex

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 11 comments
Labels: enhancement, 3 - needs review, module: uniprot, import

#111 - use try with resources

Issue - State: closed - Opened by eparejatobes over 8 years ago - 1 comment
Labels: enhancement, import

#110 - A more Java 8 code style test

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 13 comments
Labels: enhancement, import

#109 - Add proper statistics for the import process

Issue - State: closed - Opened by eparejatobes over 8 years ago - 1 comment
Labels: enhancement, question

#108 - set up Codacy

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 5 comments
Labels: enhancement

#107 - Remove GenInfo/GIs nodes and edges

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 1 comment
Labels: bug, question

#106 - use Optional properly

Issue - State: closed - Opened by eparejatobes over 8 years ago - 3 comments
Labels: enhancement, question

#105 - factor import processes into separate methods, whenever possible

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 2 comments
Labels: enhancement

#104 - Review all data import processes

Pull Request - State: closed - Opened by eparejatobes over 8 years ago - 4 comments

#103 - NCBITaxonomy scientific name parsing is broken

Pull Request - State: closed - Opened by laughedelic over 8 years ago - 1 comment
Labels: bug, module: ncbi-taxonomy

#102 - Updating bioinfo dep

Pull Request - State: closed - Opened by laughedelic about 9 years ago

#101 - Release 0.12.0-RC2

Pull Request - State: closed - Opened by eparejatobes about 9 years ago - 1 comment

#100 - Checksums for the distributions

Issue - State: closed - Opened by laughedelic over 9 years ago - 2 comments

#99 - Is there an open platform for users?

Issue - State: closed - Opened by elephantsuperjuan over 9 years ago - 5 comments
Labels: docs, question

#98 - adding proteinGeneName method to Protein

Pull Request - State: closed - Opened by pablopareja over 9 years ago

#97 - fix at ImportUniProtUniRef

Pull Request - State: closed - Opened by pablopareja over 9 years ago

#96 - adding null check for representant accession in ImportUniRef

Pull Request - State: closed - Opened by pablopareja over 9 years ago

#95 - workaround for UniRef clusters without using edges

Pull Request - State: closed - Opened by pablopareja over 9 years ago - 3 comments
Labels: 2 - in progress

#94 - YouTube channel with info about how to use UCSC browser

Issue - State: closed - Opened by marina-manrique over 9 years ago

#93 - UCSC human genome data integration

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago - 51 comments

#92 - Review docs: enzyme db

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago - 1 comment
Labels: docs

#91 - where and how are docs published?

Issue - State: closed - Opened by eparejatobes almost 10 years ago - 5 comments
Labels: docs

#90 - minor fix regarding the id showed in a logging message

Pull Request - State: closed - Opened by pablopareja almost 10 years ago

#89 - How does databases are integrated?

Issue - State: closed - Opened by Pavan637 almost 10 years ago - 1 comment

#88 - adding check for null values in ImportUniProtUniRef

Pull Request - State: closed - Opened by pablopareja almost 10 years ago

#87 - add a gitter badge to the readme

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago - 3 comments
Labels: docs

#86 - Bug at ImportUniProtUniRef

Issue - State: closed - Opened by pablopareja almost 10 years ago - 2 comments

#85 - fixt at program ImportUniProtUniRef

Pull Request - State: closed - Opened by pablopareja almost 10 years ago

#84 - Bug at ImportUniProtUniRef

Issue - State: closed - Opened by pablopareja almost 10 years ago - 1 comment

#83 - Releasing 0.12.0-RC1

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago - 1 comment

#82 - fix property types initialization

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago - 5 comments
Labels: bug

#81 - first 0.12 milestone release

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago

#80 - we still have some Uniprot in methods (instead of UniProt)

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago - 1 comment
Labels: bug, module: uniprot

#73 - Statika based deployment

Issue - State: closed - Opened by eparejatobes almost 10 years ago - 1 comment
Labels: enhancement

#70 - Regarding the documentation that must be included at this repository

Issue - State: closed - Opened by pablopareja almost 10 years ago - 8 comments
Labels: docs, enhancement

#66 - Bio4j AWS distribution

Issue - State: closed - Opened by eparejatobes almost 10 years ago - 10 comments
Labels: docs, enhancement

#65 - Examples - organize them, keep just one repo

Issue - State: closed - Opened by eparejatobes almost 10 years ago - 6 comments
Labels: enhancement

#64 - update the readme

Pull Request - State: closed - Opened by eparejatobes almost 10 years ago - 3 comments
Labels: docs, bug

#63 - Add base vertex, edge, property, ... classes for Bio4j

Issue - State: closed - Opened by eparejatobes about 10 years ago - 2 comments
Labels: enhancement, stale

#56 - bio4j 0.12

Issue - State: closed - Opened by eparejatobes about 10 years ago - 11 comments

#46 - write a Bio4j roadmap

Issue - State: closed - Opened by eparejatobes over 10 years ago
Labels: docs

#45 - Relationship between NCBI taxonomic units and EMBL

Issue - State: closed - Opened by pablopareja over 10 years ago - 10 comments
Labels: feature, enhancement, stale

#43 - Issues when modelling Uniprot taxonomy in new version

Issue - State: closed - Opened by pablopareja over 10 years ago - 12 comments
Labels: feature, enhancement, stale

#37 - Bio4j roadmap

Pull Request - State: closed - Opened by eparejatobes over 10 years ago - 1 comment
Labels: docs, enhancement