Programming
Software development: programming languages, coding, libraries and frameworks, software engineering and architecture, source control, developer tools, databases, and infrastructure.
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Open Targets Platform API platform.opentargets.org
API for target–disease associations integrating genetics, genomics, and drug data.
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PK-DB pk-db.com
Open database of experimental pharmacokinetics (PK) and ADME data from clinical and preclinical studies.
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PathwayCommons pathwaycommons.org
Database of pathways and interactions.
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SAbDab opig.stats.ox.ac.uk
Structural Antibody Database containing all antibody structures in the PDB.
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OADB (Observed Antibody Space Database) opig.stats.ox.ac.uk
Database of antibody sequences from immune repertoire sequencing.
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OmniPath omnipathdb.org
Comprehensive resource integrating protein interactions, signaling pathways, gene regulatory networks, and miRNA targets from over 100 databases.
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OMIM (Online Mendelian Inheritance in Man) omim.org
Comprehensive database of human genes and genetic disorders.
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PubMed E-utilities (esearch/efetch) nlm.nih.gov
APIs for searching and retrieving biomedical literature from PubMed.
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Human Genome Resources at NCBI ncbi.nlm.nih.gov
Database for genomics, proteomics, transcriptomics, and systems biology.
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Gene Expression Omnibus ncbi.nlm.nih.gov
Public functional genomics database.
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NCBI E-utilities ncbi.nlm.nih.gov
Unified APIs for accessing NCBI databases (Gene, GEO, SRA, PubChem, etc).
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MoNA MassBank of North America mona.fiehnlab.ucdavis.edu
Meta-database of metabolite mass spectra, metadata, and associated compounds.
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MIMIC-IV mimic.mit.edu
Freely accessible critical care database.
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MDAnalysis mdanalysis.org
Python library for analyzing and altering molecular dynamics simulation trajectories.
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MassBank massbank.jp
Open source databases and tools for mass spectrometry reference spectra.
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LIPID MAPS lipidmaps.org
Database of lipids.
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KEGG REST API kegg.jp
API for accessing KEGG pathways, compounds, genes, and reactions.
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JASPAR jaspar.genereg.net
Database of transcription factor binding profiles.
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Therapeutic Target Database idrblab.net
Drug-target, target-disease, and drug-disease datasets.
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HMDB (Human Metabolome Database) hmdb.ca
Comprehensive database of small molecule metabolites found in the human body.
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MSigDB (Molecular Signatures Database) gsea-msigdb.org
Curated gene sets derived from pathways and biological processes.
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TRRUST v2 grnpedia.org
Manually curated database of human and mouse transcriptional regulatory interactions between transcription factors and their target genes, expanded with literature-derived evidence.
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DrugBank go.drugbank.com
Database of drugs and targets (University of Alberta).
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gnomAD gnomad.broadinstitute.org
Genome Aggregation Database; genetic variation from large-scale sequencing projects.
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Drug Mechanism Database (DrugMechDB) github.com
Mechanisms of action from drug to disease.
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EU Drug Regulating Authorities Clinical Trials DB (EudraCT) eudract.ema.europa.eu
European clinical trial database.
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Pfam ebi.ac.uk
Database of protein families described by multiple sequence alignments and hidden Markov models.
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InterPro ebi.ac.uk
Protein families, domains, and functional sites database integrating 14 member databases including Pfam and PROSITE.
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IntAct ebi.ac.uk
Open-source molecular interaction database and analysis system from EMBL-EBI.
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ChEMBL Web Services ebi.ac.uk
REST API for bioactive molecules, targets, and bioassays.
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ChEBI ebi.ac.uk
Database focused on small chemical compounds.
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DisGeNET disgenet.org
Database of gene-disease associations integrating expert-curated and GWAS data.
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DISEASES diseases.jensenlab.org
Gene–disease association database integrating evidence from text mining, curated databases, and experimental data.
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CellMiner Cross Database (CellMinerCDB) discover.nci.nih.gov
Integrates multiple cancer cell line databases.
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ClinicalTrials.gov API clinicaltrials.gov
API for querying clinical trial metadata and results.
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ChemSpider chemspider.com
Chemical structure database.
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HIPPIE cbdm-01.zdv.uni-mainz.de
Human protein-protein interaction database.
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CATH database cathdb.info
Hierarchical classification of protein domain structures.
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BioCyc biocyc.org
Collection of pathway/genome databases across thousands of organisms.
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BindingDB bindingdb.org
Compounds and target database.
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AlphaFold Protein Structure Database alphafold.ebi.ac.uk
3D protein structure predictions.
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TeachOSM teachosm.org
Project assisting educators at all levels to introduce open source mapping and OpenStreetMap in the classroom. (Wiki)
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Sophox sophox.org
SPARQL API for OSM data. (Wiki)
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QLever qlever.dev
SPARQL API for OSM data. (Wiki)
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Ultra overpass-ultra.us
Web based tool for making maps with a variety of data APIs such as overpass, postpass, qlever, ohsome, sophox, and more. (Source Code)
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overpass overpass-api.de
Read-only API that serves up custom selected parts of the OSM map data. (Source Code / Wiki)
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OSMCha API osmcha.org
Powerful API that allows to query and retrieve changeset information. (Source Code)
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iD openstreetmap.org
JavaScript based editor for the web browser with a wide array of presets. (Source Code / Wiki)
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OpenGeofiction opengeofiction.net
A completely fictional user-made world map, created using the OSM software platform. (Wiki)
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Nominatim QA nominatim.org
The Nominatim Data Analyser is a QA tool used to scan the nominatim database and extract suspect data from it. These data are then presented to mappers through a visual interface so that they can correct them directly.
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