From 3ed52da8c8d8849fd84cbaec6897ed9922ea9b4a Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 8 Jun 2023 12:00:58 +0200 Subject: [PATCH] Restructure and update data (#54) * Update data * Update content and add data integrity test * Update funding and software * Update data * Update data --- .gitignore | 1 + _data/awards.yml | 4 + _data/courses.yml | 4 +- _data/databases.yml | 9 ++ _data/events.yml | 229 ++++++++++++++++++++++++++++++++++++---- _data/funding.yml | 44 ++++++-- _data/presentations.yml | 140 ------------------------ _data/software.yml | 192 +++++++++++++++++++++++---------- community.md | 6 +- research.md | 20 +++- tests/__init__.py | 0 tests/test_integrity.py | 29 +++++ 12 files changed, 444 insertions(+), 234 deletions(-) delete mode 100644 _data/presentations.yml create mode 100644 tests/__init__.py create mode 100644 tests/test_integrity.py diff --git a/.gitignore b/.gitignore index 193cd53..6b76c69 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ .sass-cache _site .jekyll-cache +*.pyc diff --git a/_data/awards.yml b/_data/awards.yml index 4ff49e7..8ce1a99 100644 --- a/_data/awards.yml +++ b/_data/awards.yml @@ -1,3 +1,7 @@ +- name: Excellence in Biocuration Early Career Award + from: International Society of Biocuration + year: 2015 + - name: Bernie Lemire Award from: Northeastern University, Department of Chemistry year: 2015 diff --git a/_data/courses.yml b/_data/courses.yml index dad4e92..82f3eed 100644 --- a/_data/courses.yml +++ b/_data/courses.yml @@ -1,4 +1,4 @@ -- name: Mechanism Enrichment Using Neurommsig +- name: Mechanism Enrichment Using NeuroMMSig level: Master's course type: Practical role: Guest Lecturer @@ -16,7 +16,7 @@ year: 2021 description: Lecture/practical on reproducibility in computational sciences -- name: Mechanism Enrichment Using Neurommsig +- name: Mechanism Enrichment Using NeuroMMSig level: Master's course type: Practical role: Guest Lecturer diff --git a/_data/databases.yml b/_data/databases.yml index 9dd53bd..4a0674b 100644 --- a/_data/databases.yml +++ b/_data/databases.yml @@ -18,6 +18,7 @@ description: Comprehensive database of identifiers, names, synonyms, cross-references, properties, and relations for biomedical entities github: biopragmatics/biolookup url: http://biolookup.io + logo: https://github.com/biopragmatics/biolookup/raw/main/src/biolookup/app/static/logo.svg - name: Bioversions github: biopragmatics/bioversions @@ -49,6 +50,14 @@ description: Curated knowledge graphs describing neurodegeneration in BEL logo: https://camo.githubusercontent.com/5efad183dee6f10de91d2cafa5e049aaba472f61/68747470733a2f2f646f63732e676f6f676c652e636f6d2f64726177696e67732f642f652f32504143582d3176535965385341384a31756c4c524671466a5832626e655f4c2d356678622d794846636a3142324a594c6b734a533930717a3879327377505a504e537277395a6a33746c6a725a696b62354b574f672f7075623f773d31353026683d313530 +- name: ComPath + language: python + github: ComPath/ComPath + url: https://compath.scai.fraunhofer.de/ + role: contributor + description: A data integration pipeline, manually curated dataset of mappings between pathway databases, and web application for integrative analysis of pathways + logo: https://avatars0.githubusercontent.com/u/36850400?s=200&v=4 + #- name: Ooh Na Na # role: creator, maintainer # description: Comprehensive metadatabase of identifiers and names for biological entities diff --git a/_data/events.yml b/_data/events.yml index 96dc4f3..64ececa 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -1,14 +1,55 @@ -- talk: https://docs.google.com/presentation/d/1oKxBzSCZGuFlIhw6jAXw00xgEGs7KgmaVR54NEdPprw/edit?usp=sharing +- talk: + invited: false + name: "Promoting the longevity of curated scientific resources through open code, open data, and public infrastructure" + url: https://docs.google.com/presentation/d/1hEryoMNyp8gwt2pvPy2ErKaw_QPvnWOmzPT0Sn4Yl4s/edit?usp=sharing + date: + day: 26 + month: April + year: 2023 + name: Biocuration 2023 + link: https://biocuration2023.github.io/ + wikidata: Q111430238 + location: + city: Padua + country: Italy + start: + day: 23 + month: April + year: 2023 + end: + day: 26 + month: April + year: 2023 + +- talk: + invited: false + name: Using dashboards to monitor ontology standardisation and community activity + url: https://docs.google.com/presentation/d/1oKxBzSCZGuFlIhw6jAXw00xgEGs7KgmaVR54NEdPprw/edit?usp=sharing name: Ontology Summit 2023 link: https://ontologforum.org/index.php/ConferenceCall_2023_02_15 - online: true + online: false date: day: 15 month: February year: 2023 -- talk: https://bit.ly/icbo2022-cth - name: International Conference on Biomedical Ontology (ICBO) 2022 +- name: 2022 Workshop on Prefixes, CURIEs, and IRIs + link: https://biopragmatics.github.io/workshops/WPCI2022.html + online: true + talk: + name: Introduction to WPCI 2022 + invited: false + url: https://docs.google.com/presentation/d/1Vq-tdq_PYSmKydKXEABElgt3oqYs_ridquHDLeUFL1A/edit?usp=sharing + date: + day: 5 + month: December + year: 2022 + +- talk: + name: The Bioregistry, CURIEs, and OBO Community Health + url: https://bit.ly/icbo2022-cth + invited: false + name: International Conference on Biomedical Ontology (ICBO) link: https://icbo-conference.github.io/icbo2022/ online: true date: @@ -16,7 +57,34 @@ month: September year: 2022 -- talk: https://bit.ly/pykeen-kgc2022 +- talk: + name: Axiomatizing Chemical Roles + url: https://bit.ly/ontologies4chem-crog + invited: true + name: Ontologies4Chem Workshop 2022 + link: https://docs.google.com/document/d/1k65sACzXh8Tt-0XV7MAwo2pPaN4YnM2BhFZRJG8fibU/edit?usp=sharing + online: true + date: + day: 7 + month: September + year: 2022 + +#- talk: +# name: "Closing the Semantic Gap: Identifying Missing Mappings and Merging Equivalent +#Concepts to Support Knowledge Graph Assembly" +# url: https://bit.ly/sorger-lab-biomappings +# invited: false +# name: Sorger Lab Meeting +# online: true +# date: +# day: 1 +# month: August +# year: 2022 + +- talk: + name: Knowledge Graph Embedding with PyKEEN in 2022 + invited: true + url: https://bit.ly/pykeen-kgc2022 name: Knowledge Graph Conference (KGC 2022) link: https://www.knowledgegraph.tech/kgc-2022/ online: true @@ -26,7 +94,10 @@ year: 2022 - link: https://graph-learning-benchmarks.github.io/glb2022 - talk: https://bit.ly/glb2022-ranking-metrics + talk: + name: "A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs" + url: https://bit.ly/glb2022-ranking-metrics + invited: false name: Graph Learning Benchmarks (GLB 2022) online: true date: @@ -45,7 +116,14 @@ - name: "Machine-Actionable Data Interoperability for Chemical Sciences (MADICES)" link: https://madices.github.io/ - talk: https://docs.google.com/presentation/d/1D0HIX41IgVdTQYKlakWcvlZvOktX23EqbLcs3LmI7mg/edit?usp=sharing + talk: + invited: true + name: "The Biopragmatics Stack: Biomedical and Chemical Semantics for Humans" + url: https://docs.google.com/presentation/d/1D0HIX41IgVdTQYKlakWcvlZvOktX23EqbLcs3LmI7mg/edit?usp=sharing + date: + day: 8 + month: February + year: 2022 online: true start: day: 7 @@ -88,6 +166,18 @@ month: November year: 2021 +- name: 2021 Workshop on Prefixes, CURIEs, and IRIs + link: https://biopragmatics.github.io/workshops/WPCI2021.html + online: true + talk: + name: Introduction to WPCI 2021 + url: https://bit.ly/WPCI2021 + invited: false + date: + day: 29 + month: October + year: 2021 + - name: RDKit User Group Meeting 2021 link: https://github.com/rdkit/UGM_2021 online: true @@ -103,7 +193,10 @@ - name: 4th Session of the International Society of Biocuration 2021 Virtual Conference online: true link: https://www.biocuration.org/14th-annual-biocuration-conference-virtual/ - poster: https://f1000research.com/posters/10-1005 + poster: + name: "Biomappings: Community Curation of Mappings between Biomedical Entities" + invited: false + url: https://f1000research.com/posters/10-1005 date: day: 5 month: October @@ -111,7 +204,10 @@ - name: Graph Machine Learning in Industry link: https://sites.google.com/view/graph-ml-in-industry/home - talk: https://www.youtube.com/watch?v=bLN1V5fZD2g&t=3665s + talk: + name: Current Issues in Theory, Reproducibility, and Utility of Graph Machine Learning in the Life Sciences + invited: true + url: https://www.youtube.com/watch?v=bLN1V5fZD2g&t=3665s wikidata: Q107633454 online: true date: @@ -121,7 +217,14 @@ - name: 12th International Conference on Biomedical Ontologies wikidata: Q108555471 - talk: https://www.youtube.com/watch?v=9Pf5wr8JxCQ&t=1s + talk: + name: "The Bioregistry: A Metaregistry for Biomedical Entities" + invited: false + url: https://www.youtube.com/watch?v=9Pf5wr8JxCQ&t=1s + date: + day: 17 + month: September + year: 2021 link: https://icbo2021.inf.unibz.it/ online: true start: @@ -141,6 +244,17 @@ month: August year: 2021 +- name: AstraZeneca + talk: + url: https://bit.ly/3wvP8yq + name: Perspectives on Knowledge Graph Embedding Models in/out of Biomedicine + invited: true + online: true + date: + day: 6 + month: April + year: 2021 + - name: INCOME Conference and Hackathon 2021 wikidata: Q104905693 online: true @@ -154,6 +268,28 @@ year: 2021 link: https://www.integrative-pathway-models.de/meetings/income2021-conference-and-hackathon/index.html +- talk: + name: Future Directions for WikiPathway Meta-curation + invited: false + url: https://docs.google.com/presentation/d/1C8T3XVOL8GiZ68WBXXSnI3SVjhd2aSBuVLXVPPGqKTw/edit?usp=sharing + name: WikiPathways Developers Conference Call + online: true + date: + day: 6 + month: January + year: 2021 + +- talk: + name: The Biological Expression Language and PyBEL in 2020 + url: https://docs.google.com/presentation/d/18ntRMvO3Q9KTX87xoLOIgqAW3iiUvxJsfEmaFh1-52A/edit?usp=sharing + invited: false + name: COVID-19 Disease Map Community Meeting + online: true + date: + day: 10 + month: July + year: 2020 + - name: 5th Disease Maps Community Meeting wikidata: Q104905357 online: true @@ -167,6 +303,17 @@ year: 2020 link: https://disease-maps.org/DMCM2020 +- talk: + name: Introduction to the Biological Expression Language and the Rational Enrichment Workflow + url: https://youtu.be/rHhuVBpoKdI + invited: true + online: true + name: CoronaWhy + date: + day: 6 + month: May + year: 2020 + - name: INCOME Hackathon 2020 wikidata: Q104905930 location: @@ -197,9 +344,24 @@ year: 2020 link: http://www.biometrische-gesellschaft.de/arbeitsgruppen/statistische-methoden-i-d-bioinformatik/workshop2020.html +- talk: + name: Applications of Knowledge Graphs in Drug Discovery + url: https://docs.google.com/presentation/d/1NQHQSD2EjOh-9XD6ffr2rDqs8AwOQ3wSBoie-e7-OXU/edit?usp=sharing + invited: true + name: Computational Drug Discovery Group, University of Leiden + location: + city: Leiden + country: Netherlands + date: + day: 5 + month: November + year: 2019 + - name: 4th Disease Maps Community Meeting wikidata: Q70206378 - poster: https://doi.org/10.6084/m9.figshare.9917753.v3 + poster: + name: Maintenance and Enrichment of Disease Maps in Biological Expression Language + url: https://doi.org/10.6084/m9.figshare.9917753.v3 location: city: Seville country: Spain @@ -213,9 +375,24 @@ year: 2019 link: https://disease-maps.org/DMCM2019 +- talk: + name: Generation and Application of Biomedical Knowledge Graphs + url: https://docs.google.com/presentation/d/11CG_Q3JrsqqKsDhl8uXP_TZzcyALhcVLvoP_pDmQ5JA/edit?usp=sharing + invited: true + name: Harvard Medical School + location: + city: Boston + country: USA + date: + day: 19 + month: July + year: 2019 + - name: The Eighth Joint Sheffield Conference on Chemoinformatics wikidata: Q64682140 - poster: https://doi.org/10.6084/m9.figshare.8288822.v2 + poster: + name: Identifying Drug Repositioning Candidates using Representation Learning on Heterogeneous Networks + url: https://doi.org/10.6084/m9.figshare.8288822.v2 location: city: Sheffield country: United Kingdom @@ -258,8 +435,11 @@ year: 2018 link: http://mldd.esat.kuleuven.be -- name: OpenBEL Community Meeting 2018 - talk: https://docs.google.com/presentation/d/1Gsk8LxrVgrICproSgWZ3Gk4BXyOg-UwFlfzhVw5O0t8/edit?usp=sharing +- name: OpenBEL Community Meeting + talk: + name: The PyBEL Ecosystem in 2018 + invited: false + url: https://docs.google.com/presentation/d/1Gsk8LxrVgrICproSgWZ3Gk4BXyOg-UwFlfzhVw5O0t8/edit?usp=sharing location: city: Boston country: USA @@ -270,8 +450,17 @@ link: http://bel.bio/conference - name: Bio-IT World - poster: https://doi.org/10.6084/m9.figshare.6231701.v1 - talk: https://docs.google.com/presentation/d/1_3j8H4f9pQ1m2ZQrF2QNfQNLh5SGqaodnl4AlaAST6w/edit?usp=sharing + poster: + name: Knowledge Assembly in Systems and Networks Biology + url: https://doi.org/10.6084/m9.figshare.6231701.v1 + talk: + name: From Knowledge Assembly to Hypothesis Generation + invited: false + url: https://docs.google.com/presentation/d/1_3j8H4f9pQ1m2ZQrF2QNfQNLh5SGqaodnl4AlaAST6w/edit?usp=sharing + date: + day: 22 + month: April + year: 2018 location: city: Boston country: USA @@ -287,7 +476,9 @@ - name: 3rd European Conference on Translational Bioinformatics wikidata: Q70206979 - poster: https://doi.org/10.6084/m9.figshare.6163775.v3 + poster: + name: "The Human Brain Pharmacome: An Overview" + url: https://doi.org/10.6084/m9.figshare.6163775.v3 location: city: Barcelona country: Spain @@ -344,7 +535,9 @@ - name: Research, Innovation and Scholarship Expo 2015 wikidata: Q104906797 link: https://www.northeastern.edu/rise - poster: https://docs.google.com/presentation/d/1FU8lWGw6x4y9A_qB9rmxSaRRKiC0V3403EJETVGYMzk/edit?usp=sharing + poster: + name: Gene Set Analysis using Phenotypic Screening Data + url: https://docs.google.com/presentation/d/1FU8lWGw6x4y9A_qB9rmxSaRRKiC0V3403EJETVGYMzk/edit?usp=sharing location: venue: Northeastern University city: Boston diff --git a/_data/funding.yml b/_data/funding.yml index 1ffdd7c..e21fd5b 100644 --- a/_data/funding.yml +++ b/_data/funding.yml @@ -8,40 +8,64 @@ url: https://discover.lanl.gov/news/1027-vaccine-development personal_start: year: 2023 - role: Grant Acquistion, Key Performer + role: Participant. Co-wrote proposal with PNNL collaborators. Responsible for design and implementation of research plan. Lead developer of semantic and analytical technologies. + money: "\\$623K (subcontract) / \\$15M overall, 2022-2024 (18 months), Grant: HDTRA1242031" + current: true -- funder: DARPA +- funder: DARPA ASKEM Program award: HR00112220036 - name: Automating Scientific Knowledge Extraction and Modeling - abbreviation: ASKEM + abbreviation: MIRA + name: "MIRA: Modeling with an Intelligent Reasoning Assistant" pi: Benjamin M. Gyori project_start: year: 2022 url: https://www.darpa.mil/news-events/2021-12-06 personal_start: year: 2022 - role: Key Performer + role: Participant + money: "\\$2.1M, 2022-2026 (42 months)" + current: true - funder: DARPA - name: Young Faculty Award + name: Young Faculty Award / DARPA Director’s Fellowship Award abbreviation: YFA pi: Benjamin M. Gyori award: W911NF2010255 url: https://govtribe.com/award/federal-grant-award/project-grant-w911nf2010255 personal_start: year: 2021 - role: Key Performer + role: Participant + money: "\\$750K, 2020-2023 (36 months)" + current: true -- name: Automating Scientific Knowledge Extraction - funder: DARPA +- name: Ecosystem of Machine-maintained Models with Automated Assembly + funder: DARPA Automating Scientific Knowledge Extraction (ASKE) / Artificial Intelligence Exploration (AIE) program abbreviation: ASKE pi: Benjamin M. Gyori url: https://govtribe.com/award/federal-contract-award/other-transaction-idv-hr00111990009 award: HR00111990009 + money: "\\$2M, 2018-2020 (18 months + extension)" project_end: year: 2022 personal_start: year: 2021 personal_end: year: 2022 - role: Supporting Performer + role: Participant + +- name: Interdisciplinary Research Award + funder: Fraunhofer Center for Machine Learning + pi: Martin Hofmann-Apitius + award: Internal + abbreviation: FML + money: "\\$40K 2019 (3 months)" + role: Key person. Co-wrote proposal. Responsible for design and implementation of research plan including applications of PyKEEN in biomedicine. + +- name: PYBEL2NDEX + funder: University of California, San Diego + pi: Martin Hofmann-Apitius + award: Contract + money: "\\$28K 2018 (6 months)" + role: Key person. Wrote proposal. Responsible for design and implementation of research plan for implementing interoperability between PyBEL and NDEx. + +#- PMI contract diff --git a/_data/presentations.yml b/_data/presentations.yml deleted file mode 100644 index a6166d3..0000000 --- a/_data/presentations.yml +++ /dev/null @@ -1,140 +0,0 @@ -- name: The Bioregistry, CURIEs, and OBO Community Health - url: https://icbo-conference.github.io/icbo2022/ - venue: International Conference on Biomedical Ontology (ICBO) 2022 - online: true - date: - day: 26 - month: September - year: 2022 - -- name: Axiomatizing Chemical Roles - url: https://docs.google.com/presentation/d/1aERfoEoTB8mWjVE0BWTJet-Ek5Y_xhESf6Z82R0U30w/edit?usp=sharing - venue: Ontologies4Chem Online Workshop - online: true - date: - day: 7 - month: September - year: 2022 - -- name: "Closing the Semantic Gap: Identifying Missing Mappings and Merging Equivalent -Concepts to Support Knowledge Graph Assembly" - url: https://bit.ly/sorger-lab-biomappings - venue: Sorger Lab Meeting - online: true - date: - day: 1 - month: August - year: 2022 - -- name: Knowledge Graph Embedding with PyKEEN in 2022 - url: https://bit.ly/pykeen-kgc2022 - venue: Knowledge Graph Conference (KGC 2022) - date: - day: 5 - month: May - year: 2022 - -- name: "A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs" - url: https://bit.ly/glb2022-ranking-metrics - venue: Graph Learning Benchmarks (GLB 2022) - date: - day: 26 - month: April - year: 2022 - -- name: "Biomappings: Community Curation of Mappings between Biomedical Entities" - url: https://f1000research.com/posters/10-1005 - venue: International Society of Biocuration 2021 Virtual Conference - online: true - date: - day: 5 - month: October - year: 2021 - -- name: Current Issues in Theory, Reproducibility, and Utility of Graph Machine Learning in the Life Sciences - url: https://bit.ly/current-issues-graphml-2021 - online: true - date: - day: 23 - month: September - year: 2021 - -- name: Perspectives on Knowledge Graph Embedding Models in/out of Biomedicine - url: https://docs.google.com/presentation/d/1JyTkf58LnK7OEiwYUtqkHXuk4n3le3-mAWSI6t4IEp8 - venue: AstraZeneca - online: true - date: - day: 6 - month: April - year: 2021 - -- name: Future Directions for WikiPathway Meta-curation - url: https://docs.google.com/presentation/d/1C8T3XVOL8GiZ68WBXXSnI3SVjhd2aSBuVLXVPPGqKTw/edit?usp=sharing - venue: WikiPathways Developers Conference Call - online: true - date: - day: 6 - month: January - year: 2021 - -- name: The Biological Expression Language and PyBEL in 2020 - url: https://docs.google.com/presentation/d/18ntRMvO3Q9KTX87xoLOIgqAW3iiUvxJsfEmaFh1-52A/edit?usp=sharing - venue: COVID-19 Disease Map Community - online: true - date: - day: 10 - month: July - year: 2020 - -- name: Introduction to the Biological Expression Language and the Rational Enrichment Workflow - url: https://youtu.be/rHhuVBpoKdI - online: true - venue: CoronaWhy - date: - day: 6 - month: May - year: 2020 - -- name: Generation and Application of Biomedical Knowledge Graphs - url: https://docs.google.com/presentation/d/11CG_Q3JrsqqKsDhl8uXP_TZzcyALhcVLvoP_pDmQ5JA/edit?usp=sharing - venue: Harvard Medical School - location: - city: Boston - country: USA - date: - day: 19 - month: July - year: 2019 - -- name: Applications of Knowledge Graphs in Drug Discovery - url: https://docs.google.com/presentation/d/1NQHQSD2EjOh-9XD6ffr2rDqs8AwOQ3wSBoie-e7-OXU/edit?usp=sharing - venue: Computational Drug Discovery Group, University of Leiden - location: - city: Leiden - country: Netherlands - date: - day: 5 - month: November - year: 2019 - -- name: The PyBEL Ecosystem in 2018 - url: https://docs.google.com/presentation/d/1Gsk8LxrVgrICproSgWZ3Gk4BXyOg-UwFlfzhVw5O0t8/edit?usp=sharing) - venue: 2018 BEL Community Meeting - location: - city: Boston - country: USA - date: - day: 18 - month: May - year: 2018 - -- name: From Knowledge Assembly to Hypothesis Generation - url: https://docs.google.com/presentation/d/1_3j8H4f9pQ1m2ZQrF2QNfQNLh5SGqaodnl4AlaAST6w/edit?usp=sharing) - venue: Bio-IT World - location: - city: Boston - county: USA - date: - day: 17 - month: May - year: 2018 diff --git a/_data/software.yml b/_data/software.yml index dd273e5..db0ecdc 100644 --- a/_data/software.yml +++ b/_data/software.yml @@ -2,95 +2,116 @@ pypi: pybel language: python github: pybel/pybel - role: creator, maintainer - description: Compiler for the Biological Expression Language + description: A compiler for the Biological Expression Language (BEL) logo: https://github.com/pybel/pybel/raw/master/docs/source/PyBEL-square-100.png wikidata: Q96470799 + roles: + - creator + - maintainer - name: Bio2BEL pypi: bio2bel language: python github: bio2bel/bio2bel - role: creator, maintainer - description: Framework for reproducible data integration in BEL + description: A framework for reproducible data integration in BEL and knowledge graph construction logo: https://github.com/bio2bel/bio2bel-art/raw/master/bio2bel-logo-100.png + roles: + - creator + - maintainer - name: BEL Commons pypi: bel-commons language: python github: bel-commons/bel-commons - role: creator, maintainer - description: Interactive exploration of networks encoded in the BEL + roles: + - creator + - maintainer + description: A web application for the interactive exploration of networks encoded in BEL logo: https://github.com/pybel/pybel-art/raw/master/BEL%20Commons/BELcommons-square-100.png -- name: PyOBO - pypi: pyobo - language: python - github: pyobo/pyobo - role: creator, maintainer - description: Harmonization of biological ontologies and controlled vocabularies - logo: /img/logos/pyobo.png - -- name: GuiltyTargets - pypi: guiltytargets - language: python - github: guiltytargets/guiltytargets - role: advisor, maintainer - description: Target prioritization framework using gene expression and network representation learning - logo: /img/logos/guiltytargets.png - name: PyKEEN pypi: pykeen language: python github: pykeen/pykeen - role: maintainer + roles: + - creator + - maintainer description: The most expansive knowledge graph embedding framework to date logo: https://raw.githubusercontent.com/pykeen/pykeen/master/docs/source/logo.png wikidata: http://www.wikidata.org/entity/Q96631404 -- name: ComPath - pypi: compath +- name: SeMRA + github: biopragmatics/semra language: python - github: ComPath/ComPath - role: contributor (core team member) - description: Platform and web application for integrating and curating pathway databases - logo: https://avatars0.githubusercontent.com/u/36850400?s=200&v=4 + pypi: semra + roles: + - creator + - maintainer + description: Automated assembly and inference of semantic mappings -- name: PathMe - pypi: pathme +- name: Bioontologies + github: biopragmatics/bioontologies language: python - github: PathwayMerger/PathMe - role: contributor (core team member) - description: Web application for exploration of pathway databases - logo: https://avatars0.githubusercontent.com/u/46240301?s=200&v=4 + pypi: bioontologies + roles: + - creator + - maintainer + description: Access and processing of ontologies on top of ROBOT and OBO Graphs -- name: Pathway Forte - pypi: pathway-forte +- name: PyOBO + pypi: pyobo language: python - github: PathwayMerger/PathMe - role: contributor (core team member) - description: Benchmarking pathway databases in functional enrichment analysis and prediction methods - logo: https://avatars3.githubusercontent.com/u/49114317?s=200& + github: pyobo/pyobo + roles: + - creator + - maintainer + description: Harmonization of biological ontologies and controlled vocabularies + logo: /img/logos/pyobo.png + +- name: curies + github: cthoyt/curies + language: python + pypi: curies + roles: + - creator + - maintainer + description: Idiomatic conversion between URIs and compact URIs (CURIEs) + +- name: GuiltyTargets + pypi: guiltytargets + language: python + github: guiltytargets/guiltytargets + roles: + - advisor + - maintainer + description: Target prioritization framework using gene expression and network representation learning + logo: /img/logos/guiltytargets.png - name: RatVec pypi: ratvec language: python github: ratvec/ratvec - role: contributor + roles: + - contributor description: Sequence-based representation learning logo: /img/logos/ratvec.png - name: PS4DR github: ps4dr/ps4dr language: r - role: advisor + roles: + - advisor + - contributor description: Drug repositioning based on bioactivity pattern matching and GWAS logo: https://avatars0.githubusercontent.com/u/51780347?s=200&v=4 - name: SeffNet github: seffnet/seffnet language: python - role: advisor, maintainer + roles: + - advisor + - contributor description: Drug repositioning framework based on network representation learning logo: https://avatars0.githubusercontent.com/u/53968086?s=200&v=4 @@ -98,7 +119,9 @@ language: python pypi: clep github: hybrid-kg/clep - role: advisor + roles: + - advisor + - contributor description: Patient stratification framework based on network representation learning logo: /img/logos/clep.jpg @@ -106,15 +129,18 @@ pypi: bel2scm language: python github: bel2scm/bel2scm - role: contributor (core team member) - description: Generation of structural causal models (SCMs) from BEL graphs + roles: + - contributor + description: Generation of structural causal models (SCMs) from BEL logo: https://avatars3.githubusercontent.com/u/67915215?s=200 -- name: y0 +- name: y0 Causal Inference Engine pypi: y0 language: python github: y0-causal-inference/y0 - role: maintainer (core team member) + roles: + - creator + - maintainer description: Representation and manipulating probabilistic expressions logo: /img/logos/y0.png @@ -122,7 +148,9 @@ pypi: stonkgs language: python github: stonkgs/stonkgs - role: advisor, contributor + roles: + - advisor + - contributor description: Multimodal Transformers for biomedical text and Knowledge Graph data logo: https://avatars.githubusercontent.com/u/81307925?s=200&v=4 @@ -130,14 +158,66 @@ pypi: chemicalx language: python github: AstraZeneca/chemicalx - role: contributor (core team member) + roles: + - contributor description: A deep learning library for drug-drug interaction, polypharmacy side effect, and synergy prediction. logo: https://github.com/AstraZeneca/chemicalx/raw/main/images/chemicalx_logo.jpg?sanitize=true -- name: RexMex - pypi: rexmex +- name: PathMe + pypi: pathme + language: python + github: PathwayMerger/PathMe + roles: + - contributor + description: Web application for exploration of pathway databases + logo: https://avatars0.githubusercontent.com/u/46240301?s=200&v=4 + +- name: Pathway Forte + pypi: pathway-forte language: python - github: AstraZeneca/rexmex - role: contributor - description: A library implementing a comprehensive collection of metrics for the evaluation of recommender systems. - logo: https://github.com/AstraZeneca/rexmex/raw/main/rexmex_small.jpg?raw=true?sanitize=true + github: PathwayMerger/PathMe + roles: + - contributor + description: Benchmarking pathway databases in functional enrichment analysis and prediction methods + logo: https://avatars3.githubusercontent.com/u/49114317?s=200& + skipcv: true + +#- name: RexMex +# pypi: rexmex +# language: python +# github: AstraZeneca/rexmex +# roles: +# - contributor +# description: A library implementing a comprehensive collection of metrics for the evaluation of recommender systems. +# logo: https://github.com/AstraZeneca/rexmex/raw/main/rexmex_small.jpg?raw=true?sanitize=true + +- name: INDRA + github: sorgerlab/indra + language: python + roles: + - contributor + description: Automated knowledge assembly and modeling in biomedicine + logo: https://indralab.github.io/images/indra_logo.png + +- name: INDRA CoGEx + github: bgyori/indra_cogex + language: python + roles: + - contributor + - maintainer + description: A $10^8$ relation-scale knowledge graph extending on causal knowledge from INDRA + +- name: MIRA + github: indralab/mira + language: python + roles: + - maintainer + description: Machine-assisted scientific modeling using meta-model templates and domain knowledge graphs + +- name: Gilda + github: indralab/gilda + language: python + roles: + - contributor + - maintainer + description: Biomedical named entity recognition and grounding using machine-learned disambiguation diff --git a/community.md b/community.md index 62b665a..ded11fc 100644 --- a/community.md +++ b/community.md @@ -18,7 +18,7 @@ permalink: /community/ @@ -98,10 +98,10 @@ My past/sporadic collaborators include: from {{ entry.start.month }} {{ entry.start.day }}-{{ entry.end.month }} {{ entry.end.day }}, {{ entry.year }} {% endif %} {% if entry.talk %} - and gave a talk + and gave a talk {% endif %} {% if entry.poster %} - and presented a poster + and presented a poster {% endif %} {% if entry.wikidata %} () diff --git a/research.md b/research.md index 2fba790..a321719 100644 --- a/research.md +++ b/research.md @@ -95,15 +95,25 @@ machine learning tasks such as subgroup identification and survival analysis. ## Presentations - + ## Publications diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_integrity.py b/tests/test_integrity.py new file mode 100644 index 0000000..ae8423c --- /dev/null +++ b/tests/test_integrity.py @@ -0,0 +1,29 @@ +from pathlib import Path +import yaml +import unittest + +HERE = Path(__file__).parent.resolve() +DATA = HERE.parent.resolve().joinpath("_data") +EVENTS_PATH = DATA.joinpath("events.yml") + + +class TestIntegrity(unittest.TestCase): + def test_events(self): + events = yaml.safe_load(EVENTS_PATH.read_text()) + for event in events: + self.assertIn("name", event) + with self.subTest(name=event['name']): + talk = event.get("talk") + if talk: + self.assertIsInstance(talk, dict) + self.assertIn("invited", talk) + self.assertIn("name", talk) + self.assertIn("url", talk) + if "date" not in event: + self.assertIn("date", talk) + poster = event.get("poster") + if poster: + self.assertIsInstance(poster, dict) + self.assertIn("name", poster) + self.assertIn("url", poster) +