Ecosyste.ms: Issues

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

GitHub / biocypher/biocypher issues and pull requests

#203 - Dependency Map

Issue - State: open - Opened by slobentanzer almost 2 years ago

#202 - McPAS

Issue - State: open - Opened by slobentanzer almost 2 years ago

#201 - IEDB

Issue - State: open - Opened by slobentanzer almost 2 years ago

#200 - VDJDB

Issue - State: open - Opened by slobentanzer almost 2 years ago

#199 - TCR-Epitope

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

#197 - Documentation: jupyter notebook and pandas output

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 3 comments

#196 - PyPy3: test and add to tutorial

Issue - State: open - Opened by slobentanzer almost 2 years ago
Labels: good first issue

#195 - GitHub action to test Windows/Linux/Mac operability

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 4 comments
Labels: good first issue

#194 - Uniprot (flat file)

Issue - State: open - Opened by slobentanzer almost 2 years ago

#193 - GTEx eQTL

Issue - State: open - Opened by slobentanzer almost 2 years ago

#192 - FAVOR (Functional Annotation of Variants)

Issue - State: open - Opened by slobentanzer almost 2 years ago

#191 - ENCODE caQTLs

Issue - State: open - Opened by slobentanzer almost 2 years ago

#190 - ENCODE CCRE

Issue - State: open - Opened by slobentanzer almost 2 years ago

#189 - ADASTRA ASB

Issue - State: open - Opened by slobentanzer almost 2 years ago

#188 - add list format to all data types for header creation

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

#187 - Memgraph

Issue - State: open - Opened by slobentanzer almost 2 years ago

#184 - Write some documentation about BioCypher's handling of identifiers

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

#183 - Documentation: make autodoc work for all modules

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

#182 - Single cell ontology mapping KG

Issue - State: open - Opened by slobentanzer almost 2 years ago

#181 - Cell Ontology (CL)

Issue - State: open - Opened by slobentanzer almost 2 years ago

#180 - `_write.py`: better separate actual write directory from import call file prefix

Issue - State: open - Opened by slobentanzer almost 2 years ago
Labels: enhancement

#179 - output modularisation

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

#178 - ArangoDB

Issue - State: open - Opened by slobentanzer almost 2 years ago

#177 - GSK neointerface as connect method

Issue - State: open - Opened by slobentanzer almost 2 years ago
Labels: enhancement

#176 - Oncodash KB

Issue - State: open - Opened by slobentanzer almost 2 years ago

#175 - LIANA KG

Issue - State: open - Opened by slobentanzer almost 2 years ago

#174 - Skip fixture not working for driver

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment

#173 - Tail ontologies: choice of merging or joining the nodes (`merge_nodes`)

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment
Labels: enhancement

#172 - DDInter

Issue - State: open - Opened by bnymnsen almost 2 years ago

#171 - ChEMBL

Issue - State: open - Opened by bnymnsen almost 2 years ago

#170 - CTD (Comparative Toxicogenomics Database)

Issue - State: open - Opened by bnymnsen almost 2 years ago - 4 comments

#169 - DGIdb

Issue - State: open - Opened by bnymnsen almost 2 years ago

#168 - Pharos

Issue - State: open - Opened by bnymnsen almost 2 years ago

#167 - Drugbank

Issue - State: open - Opened by bnymnsen almost 2 years ago

#166 - InterPro

Issue - State: open - Opened by bnymnsen almost 2 years ago

#165 - Biomedical Resource Ontology (BRO)

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment

#164 - GitHub API

Issue - State: open - Opened by slobentanzer almost 2 years ago

#163 - BioCypher meta graph

Issue - State: open - Opened by slobentanzer almost 2 years ago

#162 - Modularisation of BatchWriter and PostgreSQL adaptation

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

#161 - Rename nodes/edges in code to avoid confusion

Issue - State: open - Opened by vincentvialard almost 2 years ago

#160 - Nodes with edges

Pull Request - State: closed - Opened by vincentvialard almost 2 years ago - 3 comments

#159 - Template for BioCypher gives error

Issue - State: closed - Opened by Valentijn000 almost 2 years ago - 5 comments

#158 - Open Targets community KG

Issue - State: open - Opened by slobentanzer almost 2 years ago

#157 - NeDRex

Issue - State: open - Opened by slobentanzer almost 2 years ago

#156 - MONDO Disease Ontology

Issue - State: open - Opened by slobentanzer almost 2 years ago

#155 - Biomedical Resource Ontology

Issue - State: open - Opened by slobentanzer almost 2 years ago - 3 comments

#154 - Disease Ontology (DO)

Issue - State: open - Opened by slobentanzer almost 2 years ago

#153 - PostgreSQL

Issue - State: open - Opened by slobentanzer almost 2 years ago

#152 - Sequence Ontology (SO)

Issue - State: open - Opened by slobentanzer almost 2 years ago

#151 - Neo4j

Issue - State: open - Opened by slobentanzer almost 2 years ago

#150 - STITCH

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

#149 - HMDB

Issue - State: open - Opened by slobentanzer almost 2 years ago

#148 - metalinks

Issue - State: open - Opened by slobentanzer almost 2 years ago

#146 - Modularise

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

#143 - OmniPath

Issue - State: open - Opened by slobentanzer almost 2 years ago

#142 - Abstract base class for batch writer

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment

#141 - YAML spec: single vs double quote and escape

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment
Labels: bug, enhancement

#140 - Exotic delimiters such as ¦ (broken pipe): can we use them?

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment
Labels: question

#137 - Add deduplicator class

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 2 comments
Labels: enhancement

#135 - Monarch flat file

Issue - State: open - Opened by slobentanzer almost 2 years ago

#131 - Disk writer interface implementation

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 2 comments
Labels: enhancement

#128 - GitHub Action: deprecation warning of `save-state`

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment
Labels: enhancement

#127 - Human Reference Atlas (HRA)

Issue - State: open - Opened by slobentanzer almost 2 years ago

#126 - Step "Translating BioCypher config leaves to Biolink" fails

Issue - State: open - Opened by AndiMajore almost 2 years ago - 2 comments
Labels: enhancement

#125 - STRING

Issue - State: open - Opened by bnymnsen almost 2 years ago

#124 - BioGRID

Issue - State: open - Opened by bnymnsen almost 2 years ago

#123 - IntAct

Issue - State: open - Opened by bnymnsen almost 2 years ago - 3 comments

#122 - PPI Adapter

Issue - State: open - Opened by bnymnsen almost 2 years ago - 3 comments

#121 - RDF (Resource Description Framwork)

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment

#120 - NIH Funding Knowledge Graph

Issue - State: open - Opened by slobentanzer almost 2 years ago

#119 - miRBase

Issue - State: open - Opened by slobentanzer almost 2 years ago
Labels: good first issue

#118 - OBO Foundry Ontologies

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

#117 - Biolink

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

#116 - TopLD

Issue - State: open - Opened by slobentanzer almost 2 years ago

#115 - gnomAD

Issue - State: open - Opened by slobentanzer almost 2 years ago

#114 - GENCODE

Issue - State: open - Opened by slobentanzer almost 2 years ago

#113 - ENCODE eQTLs

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment

#112 - IGVF: Impact of Genomic Variation on Function

Issue - State: open - Opened by slobentanzer almost 2 years ago

#111 - UniProt (API)

Issue - State: open - Opened by slobentanzer almost 2 years ago - 4 comments

#107 - Allow hybridisation of arbitrarily many ontologies

Issue - State: closed - Opened by slobentanzer almost 2 years ago
Labels: enhancement

#106 - RDF

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

#103 - The new edge implementation recurses

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 3 comments
Labels: bug

#102 - Command from driver.write_import_call() does not work in Neo4j 5.x

Issue - State: closed - Opened by dgg32 almost 2 years ago - 3 comments
Labels: enhancement, good first issue

#99 - `driver.summary()` method to wrap convenience methods

Issue - State: closed - Opened by slobentanzer almost 2 years ago - 1 comment
Labels: enhancement

#97 - miRNA data integration portal (mirDIP)

Issue - State: open - Opened by slobentanzer almost 2 years ago

#95 - Allow multiple edge type creation

Pull Request - State: closed - Opened by bnymnsen about 2 years ago - 5 comments

#89 - Simplify and standardise interface in adapter for node/edge types fields

Issue - State: open - Opened by slobentanzer about 2 years ago
Labels: enhancement

#88 - BioCypher `pipeline`

Issue - State: open - Opened by slobentanzer about 2 years ago - 4 comments
Labels: enhancement

#85 - drugst.one

Issue - State: open - Opened by slobentanzer about 2 years ago - 3 comments

#83 - Implement Neo4j v5 incremental admin import

Issue - State: closed - Opened by slobentanzer about 2 years ago - 1 comment
Labels: enhancement

#81 - Move from tuples to BioCypher classes in the adapter input fields

Issue - State: open - Opened by slobentanzer about 2 years ago - 6 comments
Labels: enhancement

#77 - Alert user to detached nodes in ontology graph

Issue - State: closed - Opened by slobentanzer about 2 years ago - 1 comment
Labels: enhancement

#65 - Allow synonyms for ontology classes

Issue - State: closed - Opened by slobentanzer about 2 years ago

#64 - Bioteque

Issue - State: open - Opened by slobentanzer about 2 years ago

#61 - TUM AI

Issue - State: open - Opened by slobentanzer over 2 years ago

#55 - Write ontological backbone to graph

Issue - State: open - Opened by slobentanzer over 2 years ago
Labels: enhancement

#52 - Represent the Biolink hierarchy as an abstract data model akin to pydantic in python directly

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