Ecosyste.ms: Issues

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GitHub / biocypher/biocypher issues and pull requests

#412 - feat(write): OWL

Pull Request - State: open - Opened by jdreo 12 days ago - 7 comments

#411 - Ad-hoc generation of ontologies as a service

Issue - State: open - Opened by slobentanzer 13 days ago

#410 - feat(neo4j): allow several labels sorting methods

Pull Request - State: closed - Opened by jdreo 15 days ago

#409 - update github action config:

Pull Request - State: closed - Opened by slobentanzer 18 days ago

#408 - Add option to load resource download definition from config

Issue - State: open - Opened by slobentanzer 18 days ago - 1 comment
Labels: enhancement

#407 - [Bug]: RDF support

Issue - State: open - Opened by jdreo 19 days ago - 4 comments
Labels: enhancement

#405 - Fix neo4j CSV output not escaping quote character and cause import error

Pull Request - State: closed - Opened by kpto about 1 month ago - 2 comments
Labels: bug

#404 - Upgrade CI components to Python 3.11 default

Issue - State: open - Opened by slobentanzer about 1 month ago

#403 - Dev-networkx-ruff

Pull Request - State: closed - Opened by slobentanzer about 1 month ago - 2 comments

#402 - Feature-networkx-output

Pull Request - State: closed - Opened by slobentanzer about 1 month ago

#401 - Feature networkx output

Pull Request - State: closed - Opened by ryxx0811 about 1 month ago - 1 comment

#397 - Upgrade documentation

Issue - State: open - Opened by slobentanzer 3 months ago

#395 - Implement Ruff linting

Issue - State: closed - Opened by slobentanzer 3 months ago

#393 - Docker compose on Windows: paths / characters failure

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

#392 - Add volume purge to the docker build script

Issue - State: open - Opened by slobentanzer 3 months ago

#391 - Update docstring of BioCypherEdge class

Issue - State: open - Opened by slobentanzer 3 months ago

#389 - Rename `preferred_id` to `namespace`

Issue - State: open - Opened by slobentanzer 4 months ago

#386 - DFG project 528753569

Issue - State: open - Opened by slobentanzer 4 months ago

#385 - Open Targets project OTAR3088

Issue - State: open - Opened by slobentanzer 4 months ago

#382 - Add web page monitoring

Issue - State: closed - Opened by slobentanzer 4 months ago - 1 comment

#381 - Cache the ontology files

Issue - State: open - Opened by slobentanzer 4 months ago

#380 - Adhere to SPEC 0

Issue - State: open - Opened by slobentanzer 4 months ago

#379 - Folder for drawio diagrams

Pull Request - State: closed - Opened by ecarrenolozano 4 months ago - 31 comments

#378 - Folder for diagrams in biocypher/docs

Pull Request - State: closed - Opened by ecarrenolozano 4 months ago

#375 - Create config.yml

Pull Request - State: closed - Opened by slobentanzer 5 months ago

#374 - Graph nodes Semantic search

Issue - State: open - Opened by winternewt 5 months ago - 2 comments

#373 - Properties of duplicate nodes

Issue - State: closed - Opened by mbaric758 6 months ago - 5 comments

#372 - update to api request caching and doc

Pull Request - State: closed - Opened by ryxx0811 6 months ago

#371 - Related to #296:Resource download with parameter

Pull Request - State: closed - Opened by ryxx0811 6 months ago - 2 comments

#370 - Mock downloads in _get module tests

Issue - State: open - Opened by slobentanzer 6 months ago - 1 comment

#369 - add function for caching API requests and refine the args description

Pull Request - State: closed - Opened by ryxx0811 6 months ago - 2 comments

#368 - Boolean sometimes not imported correctly (all 'false')

Issue - State: open - Opened by slobentanzer 6 months ago - 1 comment

#367 - Duplicate removal in Open-Targets Data.

Issue - State: closed - Opened by rahulmaurya1507 7 months ago - 2 comments

#366 - Update supported Python versions in the Readme

Issue - State: closed - Opened by nilskre 7 months ago - 2 comments
Labels: good first issue

#365 - fix(import_call):Database name after import prefix

Pull Request - State: closed - Opened by mbaric758 7 months ago - 12 comments

#363 - Error importing csv files with Neo4j v.5.21.2

Issue - State: closed - Opened by mbaric758 7 months ago - 3 comments

#361 - Streamline output api

Pull Request - State: closed - Opened by nilskre 7 months ago - 26 comments

#360 - Allow for time stamped directories as used in some of the examples

Pull Request - State: closed - Opened by Mjvolk3 7 months ago - 9 comments

#358 - Directly get in memory networkx graph from BioCypher

Issue - State: open - Opened by nilskre 8 months ago - 5 comments

#357 - Close component issues

Issue - State: open - Opened by slobentanzer 8 months ago - 1 comment

#356 - The BioCypher meta-graph link in the documentation appears to be down

Issue - State: open - Opened by tskir 8 months ago - 1 comment

#354 - Automatically ensure that docstrings are up to date

Issue - State: open - Opened by nilskre 8 months ago - 4 comments
Labels: good first issue

#353 - Not existing method start_ontology are called from core methods

Issue - State: open - Opened by nilskre 8 months ago - 1 comment

#352 - Networkx and csv output adapter

Pull Request - State: closed - Opened by nilskre 8 months ago

#351 - Neo4j version specification via config

Issue - State: open - Opened by slobentanzer 8 months ago

#350 - Neo4j v5: incremental admin import

Issue - State: open - Opened by slobentanzer 8 months ago

#348 - Pandas/CSV

Issue - State: closed - Opened by nilskre 9 months ago

#347 - networkx

Issue - State: closed - Opened by nilskre 9 months ago

#345 - PyG HeteroData

Issue - State: open - Opened by nilskre 9 months ago

#344 - iRefIndex - new adapter

Issue - State: open - Opened by abotzki 9 months ago - 1 comment

#342 - CI: Python 3.9 not on MacOS latest any more, but 3.12 also fails

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

#341 - Create full ETL for RDF type output

Issue - State: open - Opened by LoesvdBiggelaar 10 months ago
Labels: enhancement

#339 - Run Neo4j v4 test action only on Linux (legacy)

Issue - State: closed - Opened by slobentanzer 10 months ago

#338 - Rdf output adapter

Pull Request - State: closed - Opened by slobentanzer 10 months ago - 6 comments

#337 - first version of RDF conversion

Pull Request - State: closed - Opened by LoesvdBiggelaar 10 months ago - 13 comments

#336 - #321: fix cicd pipeline

Pull Request - State: closed - Opened by nilskre 10 months ago - 1 comment

#335 - [Feature request] Support for long neo4j-admin database import

Issue - State: open - Opened by JPonsa 11 months ago - 3 comments

#334 - Relational constraints to SQLLITE output

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

#332 - Refactoring: include neo4j-utils in BioCypher core

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

#331 - error occurred when use poetry add biocypher

Issue - State: open - Opened by willy20040711 11 months ago - 1 comment

#329 - refactor(write): return the path of the import call file

Pull Request - State: closed - Opened by jdreo 11 months ago - 1 comment

#328 - doc(error messages): more detailled errors

Pull Request - State: closed - Opened by jdreo 11 months ago - 1 comment

#327 - Ontology reverse id label yaml config

Pull Request - State: closed - Opened by nilskre 11 months ago - 1 comment

#326 - Add unit tests to template repo

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

#325 - #273: add unit test for duplicated tail ontologies

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

#324 - Log real path of the `schema_config.yaml` on startup

Issue - State: closed - Opened by nilskre 11 months ago

#323 - Sqlite output adapter

Pull Request - State: closed - Opened by nilskre 12 months ago

#321 - Neo4j version 5 patch

Pull Request - State: closed - Opened by mbaric758 12 months ago - 15 comments

#320 - Head join node not found in head ontology

Issue - State: closed - Opened by clairelaudy 12 months ago - 7 comments

#318 - RDF parsing leads to `none` type nodes

Issue - State: open - Opened by slobentanzer 12 months ago

#317 - Add a document for building Pole standalone Docker image

Pull Request - State: closed - Opened by fengsh27 12 months ago

#315 - bin/neo4j-admin import not working in latest DBMS 5.15

Issue - State: closed - Opened by JPonsa 12 months ago - 2 comments

#314 - SQLite

Issue - State: closed - Opened by nilskre 12 months ago - 3 comments

#313 - Ontology: Make reverse_labels configurable via biocypher_config.yaml

Issue - State: closed - Opened by nilskre about 1 year ago - 1 comment

#312 - Neo4j parsing: replace dots with underscores categorically

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

#311 - #310: improve runtime of rdflib to networkx transformation

Pull Request - State: closed - Opened by nilskre about 1 year ago - 3 comments

#310 - Ontology: Improve performance of rdflib -> networkx graph

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

#309 - Brackets in ontology names

Pull Request - State: closed - Opened by nilskre about 1 year ago - 5 comments

#308 - Bugfix ontology multiple parents

Pull Request - State: closed - Opened by nilskre about 1 year ago - 11 comments