From 5b47cfbd6a3dee858a6117ce7af48d0d2d7d0fa4 Mon Sep 17 00:00:00 2001 From: Larry Chung Date: Wed, 11 Sep 2024 16:26:42 -0400 Subject: [PATCH] Molepro docs (#85) * Create molecular-data.md * Update molecular-data.md Information from the wiki athttps://github.com/NCATSTranslator/Translator-All/wiki/Molecular-Data-Provider * Update molecular-data.md Fixed linkout to MolePro Github --- docs/architecture/kp/molecular-data.md | 84 ++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 docs/architecture/kp/molecular-data.md diff --git a/docs/architecture/kp/molecular-data.md b/docs/architecture/kp/molecular-data.md new file mode 100644 index 0000000..4cd68f6 --- /dev/null +++ b/docs/architecture/kp/molecular-data.md @@ -0,0 +1,84 @@ +[**Back to Home**](https://github.com/NCATSTranslator/NCATSTranslator.github.io/wiki) + +# Molecular Data Provider (KP) + +## General Description +The Molecular Data Provider, known as MolePro, is part of the NCATS Biomedical Data Translator project. MolePro integrates diverse chemical biology data sources and provides a curated framework for chemical entities, enhancing our understanding of their effects on biological targets. + +Key features of MolePro include: + +1. **Data Integration**: MolePro consolidates information from various public chemical biology datasets, portals, and tools to offer comprehensive insights into compounds and their protein targets. This includes similarity-based connections. + +2. **Unbiased Approach**: We adhere to a stringent policy to avoid expert bias, ensuring true innovation. Our process involves impartial data scouting, efficient architecture building, and meticulous data provenance capturing. + +3. **Unified Framework**: The result is a cohesive framework for compounds and targets, facilitating the identification of new compounds or targets through "guilt-by-association" inferences from large datasets. + +4. **Chemical Biology Expertise**: MolePro contributes to the Translator project with expertise with probes in drug-discovery, toxicity flagging, and small-molecule mechanism of action elucidation. + +MolePro harnesses powerful and diverse datasets to support research and development in chemical biology, ultimately aiming to deepen our understanding and application of chemical entities in biomedical science. + +## Team Contact: + +translator@broadinstitute.org + +Vlado Dancik ([@vdancik](https://github.com/vdancik)) + +# Interfaces +MolePro was designed to provide the same molecular data knowledge in a choice of two APIs to cater to various user preferences: the MolePro API and the TRAPI. + +### MolePro API +We have made MolePro's knowledge graph accessible to the scientific community through the MolePro API hosted on two servers: +* NCATS Translator server: https://molepro.transltr.io/molecular_data_provider/api +* Broad Institute server: https://translator.broadinstitute.org/molecular_data_provider/api + +### Translator Reasoner API + +MolePro can communicate biomedical questions and answers using the standardized Translator Reasoner API (TRAPI). Adhering to the TRAPI standard, MolePro integrates the query graph, knowledge graph, and results into a single HTTP message. Consequently, MolePro's knowledge graph is accessible to the scientific community through the TRAPI hosted on two servers: +* NCATS Translator server: https://molepro-trapi.transltr.io/molepro/trapi/v1.5/ui/ +* Broad Institute server: https://translator.broadinstitute.org/molepro/trapi/v1.5/ui/ + +# Knowledge Sources +MolePro's knowledge graph is constructed through extensive data scouting and careful data wrangling, integrating information from over two dozen discovered knowledge sources, including: +* _BiGG Models_ http://bigg.ucsd.edu/ +* _BigGIM_ http://biggim.ncats.io/api/ +* _BindingDB_ https://www.bindingdb.org/ +* _ChEBI_ https://www.ebi.ac.uk/chebi +* _ChemBank_ http://chembank.broadinstitute.org/ +* _ChEMBL_ https://www.ebi.ac.uk/chembl/ +* _CMAP_ https://clue.io/ +* _CTD_ http://ctdbase.org/ +* _CTRP_ http://portals.broadinstitute.org/ctrp/ +* _DepMap_ https://depmap.org/portal/ +* _DGIdb_ http://dgidb.org/ +* _DrugBank_ https://www.drugbank.ca/ +* _DrugCentral_ http://drugcentral.org/privacy +* _Drug Repurposing Hub_ https://clue.io/repurposing +* _DSSTox_ https://www.epa.gov/comptox-tools/distributed-structure-searchable-toxicity-dsstox-database +* _Gelinea_ https://github.com/broadinstitute/GeLiNEA +* _GtoPdb_ https://www.guidetopharmacology.org/ +* _HGNC_ https://www.genenames.org +* _HMDB_ https://www.hmdb.ca/ +* _Inxight:Drugs_ https://drugs.ncats.io/ +* _Kinomescan_ https://lincs.hms.harvard.edu/kinomescan/ +* _MSigDB_ https://www.gsea-msigdb.org/gsea/msigdb/index.jsp +* _PharmGKB_ https://www.pharmgkb.org/ +* _Pharos_ https://pharos.nih.gov +* _ProbeMiner_ https://probeminer.icr.ac.uk/#/ +* _PubChem_ https://pubchem.ncbi.nlm.nih.gov/ +* _Reactome_ https://reactome.org/ +* _RxNorm_ https://www.nlm.nih.gov/research/umls/rxnorm/index.html +* _SIDER_ http://sideeffects.embl.de/ +* _STITCH_ http://stitch.embl.de +* _STRING_ https://string-db.org/ + + +For additional details about ingested data source see [Catalog of MolePro knowledge sources](https://translator.broadinstitute.org/molecular_data_provider/transformers) (JSON formatted output). + +# Source Code + +[MolePro GitHub](https://github.com/broadinstitute/molecular-data-provider) + +# External Documentation + +[Additional MolePro documentation in GitHub](https://github.com/broadinstitute/molecular-data-provider) +