Ecosyste.ms: Issues

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

GitHub / monarch-initiative/owlsim-v3 issues and pull requests

#109 - Bump gson from 2.2.4 to 2.8.9 in /owlsim-core/bin

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#108 - Bump gson from 2.2.4 to 2.8.9 in /owlsim-core

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#107 - Bump jena-core from 2.11.2 to 4.2.0 in /owlsim-core/bin

Pull Request - State: open - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#106 - Bump jena-core from 2.11.2 to 4.2.0 in /owlsim-core

Pull Request - State: open - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#105 - Migrate to central logging

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

#103 - Add request-level logging for long-running queries

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

#102 - Bump commons-io from 2.2 to 2.7 in /owlsim-core/bin

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#101 - Bump commons-io from 2.2 to 2.7 in /owlsim-core

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#100 - Bump ant from 1.8.2 to 1.10.9 in /owlsim-core

Pull Request - State: open - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#99 - Bump ant from 1.8.2 to 1.10.9 in /owlsim-core/bin

Pull Request - State: open - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#98 - Bump junit from 4.12 to 4.13.1

Pull Request - State: open - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#97 - Bump ant from 1.8.2 to 1.9.15 in /owlsim-core/bin

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#96 - Bump ant from 1.8.2 to 1.9.15 in /owlsim-core

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#95 - Monarch OwlSim API is timing out.

Issue - State: closed - Opened by monicacecilia almost 6 years ago - 2 comments

#94 - Documentation of similarity measures (and REST services)

Issue - State: open - Opened by matentzn almost 7 years ago

#93 - Building javadoc fails due to missing parameter descriptions

Issue - State: open - Opened by matentzn almost 7 years ago

#92 - Phenotype sort

Issue - State: open - Opened by jmcmurry about 7 years ago - 1 comment

#91 - Use requests in golr exporter

Pull Request - State: closed - Opened by kshefchek over 7 years ago - 2 comments

#90 - Low phenodigm scores for disease matching

Issue - State: open - Opened by kshefchek over 7 years ago

#89 - Explore many-to-many matches for profiles

Issue - State: open - Opened by jmcmurry over 7 years ago - 3 comments

#87 - Add prefix filter to service layer

Issue - State: open - Opened by kshefchek almost 8 years ago

#86 - For Hs configuration, add option for diseases and genes

Issue - State: closed - Opened by kshefchek almost 8 years ago - 1 comment
Labels: enhancement

#85 - Factor in phenotype frequency

Issue - State: closed - Opened by jmcmurry almost 8 years ago - 1 comment

#84 - Docker image root ontology

Issue - State: open - Opened by jnguyenx almost 8 years ago
Labels: enhancement

#83 - Command error in repository Readme

Issue - State: closed - Opened by ManavalanG almost 8 years ago - 1 comment

#82 - 58 docker biolink update

Pull Request - State: closed - Opened by jnguyenx almost 8 years ago
Labels: enhancement

#80 - Consider p value calculation for IC based sim calculations

Issue - State: open - Opened by kshefchek almost 8 years ago - 2 comments
Labels: question

#79 - [#78] allow labels to be loaded as tsvs

Pull Request - State: closed - Opened by jnguyenx almost 8 years ago
Labels: enhancement

#78 - Add a way to load label tsv along with data tsv

Issue - State: closed - Opened by jnguyenx almost 8 years ago
Labels: enhancement

#77 - Implementing meta-information for annotations of objects

Issue - State: closed - Opened by drseb almost 8 years ago - 6 comments
Labels: enhancement, help wanted, question

#76 - Implemented prefix filter,

Pull Request - State: closed - Opened by cmungall almost 8 years ago

#75 - Add additional filters for match service

Issue - State: open - Opened by kshefchek almost 8 years ago

#74 - implemented a simple boolean matcher.

Pull Request - State: open - Opened by cmungall almost 8 years ago - 2 comments

#73 - [#72] added service for single entity

Pull Request - State: closed - Opened by jnguyenx almost 8 years ago - 3 comments

#72 - add ontomatch: 1 entity vs ontology

Issue - State: closed - Opened by jnguyenx almost 8 years ago - 1 comment

#71 - Adding ability to load individuals from in-memory data as well as off-disk.

Pull Request - State: closed - Opened by julesjacobsen almost 8 years ago - 7 comments

#70 - 57 loader refactor

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

#69 - Add paging to ontomatch service

Issue - State: open - Opened by cmungall almost 8 years ago - 5 comments

#68 - WIP: Adding metadata required for release on mvncentral

Pull Request - State: open - Opened by cmungall almost 8 years ago

#67 - [#58] Added Dockerfile

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

#66 - Unecessary auto-(un)boxing of intgers in BMKnowledgeBaseOWLAPIImpl

Issue - State: closed - Opened by julesjacobsen almost 8 years ago - 1 comment

#65 - Provide better documentation for how to use owlsim-v3 as a java library

Issue - State: open - Opened by cmungall almost 8 years ago - 1 comment

#64 - [#62] moved guice modules away from core

Pull Request - State: closed - Opened by jnguyenx almost 8 years ago

#63 - Make specific routes for the different matchers

Issue - State: open - Opened by cmungall almost 8 years ago

#62 - Leakage of owlsim-server guice configuration into owlsim-core

Issue - State: closed - Opened by julesjacobsen almost 8 years ago - 7 comments

#61 - ProfileMatcher should have a isNegationAware method

Issue - State: open - Opened by julesjacobsen almost 8 years ago

#60 - WIP: first pass at frequency-awareness

Pull Request - State: closed - Opened by cmungall almost 8 years ago - 6 comments

#59 - Add capability to breakdown similarity results by symptom or high level terms

Issue - State: open - Opened by cmungall almost 8 years ago - 1 comment

#58 - Docker file / image for owlsim3 server

Issue - State: closed - Opened by tudorgroza almost 8 years ago - 2 comments
Labels: enhancement

#57 - Refactor or better document loaders

Issue - State: open - Opened by cmungall almost 8 years ago - 10 comments

#56 - Implement bayesian frequency awareness

Issue - State: open - Opened by cmungall almost 8 years ago - 5 comments
Labels: R24

#55 - Align with drseb code

Issue - State: open - Opened by cmungall almost 8 years ago

#54 - Allow querying by individual id

Issue - State: open - Opened by cmungall almost 8 years ago

#53 - Empty matches with simple configuration file

Issue - State: open - Opened by jnguyenx almost 8 years ago - 1 comment
Labels: bug

#52 - [#44] almost working generated json. Blocked by a swagger-core bug

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

#50 - Unused code elements in NaiveBayesFixedWeightThreeStateProfileMatcher

Issue - State: open - Opened by drseb about 8 years ago - 2 comments

#49 - change method-name converIndexSetToBitmap to convertIndexSetToBitmap

Pull Request - State: closed - Opened by drseb about 8 years ago

#48 - [#44] smartapi reported errors

Pull Request - State: closed - Opened by jnguyenx about 8 years ago

#47 - swagger update

Pull Request - State: closed - Opened by jnguyenx about 8 years ago - 2 comments
Labels: bug, enhancement

#46 - Update swagger to fix encoding issue

Issue - State: closed - Opened by jnguyenx about 8 years ago

#45 - Port annotation sufficiency from owlsim2

Issue - State: closed - Opened by cmungall about 8 years ago - 1 comment

#44 - Register with smart API

Issue - State: open - Opened by cmungall about 8 years ago - 1 comment

#43 - Add routes to service to introspect details of loaded ontologies

Issue - State: open - Opened by cmungall about 8 years ago - 1 comment

#42 - Adding enrichment service

Pull Request - State: closed - Opened by cmungall about 8 years ago

#41 - matching between ontology classes (not instances)

Pull Request - State: closed - Opened by cmungall about 8 years ago

#38 - services: return more informative error messages

Issue - State: open - Opened by cmungall about 8 years ago

#37 - 24 curie

Pull Request - State: closed - Opened by jnguyenx about 8 years ago

#36 - [#33] configure Jackson to ignore empty beans

Pull Request - State: closed - Opened by jnguyenx about 8 years ago

#35 - too much logging info

Issue - State: open - Opened by cmungall about 8 years ago

#34 - services: change parameter names in match

Issue - State: open - Opened by cmungall about 8 years ago

#33 - swagger is producing invalid json

Issue - State: closed - Opened by cmungall about 8 years ago - 1 comment

#32 - Add compare attribute sets to REST service layer

Issue - State: closed - Opened by kshefchek about 8 years ago - 2 comments

#30 - Phenopacket reading

Pull Request - State: open - Opened by balhoff over 8 years ago - 3 comments

#29 - Fixed error from import of missing class.

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

#28 - Read phenopackets

Issue - State: open - Opened by balhoff over 8 years ago - 4 comments

#27 - Add OMIA species to OwlSim calculations

Issue - State: open - Opened by jmcmurry over 8 years ago
Labels: enhancement

#26 - Error running Makefile

Issue - State: open - Opened by balhoff over 8 years ago - 3 comments

#25 - Test resource missing

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

#24 - Implement CURIE handling

Issue - State: closed - Opened by cmungall almost 9 years ago - 11 comments

#23 - Full test v3 vs v2 for both speed and accuracy

Issue - State: open - Opened by cmungall almost 9 years ago

#22 - Bridge to owlsim2 service layer

Issue - State: open - Opened by cmungall almost 9 years ago

#21 - RoaringBitmaps?

Issue - State: open - Opened by julesjacobsen almost 9 years ago - 1 comment
Labels: question

#20 - Reciprocal ranking of models

Issue - State: open - Opened by jmcmurry about 9 years ago - 1 comment

#19 - adding owlsim logos for light/dark backgrounds

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

#18 - testSelfComparisonKS in ICDistributionTest sometimes fails

Issue - State: open - Opened by cmungall over 9 years ago

#17 - Adding labels to phenotype list

Issue - State: open - Opened by yuanzhou over 9 years ago

#16 - Should MatcherModule move from services to core?

Issue - State: closed - Opened by cmungall over 9 years ago - 4 comments
Labels: question

#15 - ICDistributionTest.testSelfComparisonKS sometimes fails

Issue - State: open - Opened by cmungall over 9 years ago

#14 - add license

Issue - State: open - Opened by nlwashington almost 10 years ago - 3 comments

#13 - Handling apparent contradicitions with negation data

Issue - State: open - Opened by cmungall almost 10 years ago - 11 comments
Labels: R24

#12 - Move repo to monarch org

Issue - State: closed - Opened by cmungall almost 10 years ago

#10 - refactor Matchers with Comparator methods

Issue - State: open - Opened by nlwashington about 10 years ago - 5 comments
Labels: enhancement