What question did this study set out to answer?

Update the STITCH database to broaden protein-chemical interaction coverage, incorporate full-text mining and structure-based predictions, and facilitate direct integration of custom user datasets.

November 28, 2013Nucleic Acids ResearchOpen Access

STITCH 4: integration of protein–chemical interactions with user data

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Authors

MKMichael KuhnEuropean Molecular Biology Laboratory DSDamian SzklarczykSIB Swiss Institute of Bioinformatics SPSune Pletscher-FrankildClinical Microbiomics (Denmark)

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Implication

Database update reports an expanded network of protein-chemical interactions and user-data integration, highlighting enhanced functional annotation across diverse organisms.

Key Points

Update the STITCH database to broaden protein-chemical interaction coverage, incorporate full-text mining and structure-based predictions, and facilitate direct integration of custom user datasets.
Expanded literature text-mining pipelines to scan full-text articles and implemented prediction algorithms based on chemical structures.
Restructured cross-species interaction transfer to depend strictly on orthology rather than broad sequence similarity, excluding transfers to paralogous proteins.
Engineered upload interfaces supporting internal identifiers, chemical structures, and quantitative screening hit lists via a web interface, an API, and downloadable files.
Expanded total database content to 390,000 chemicals and 3.6 million proteins spanning 1,133 organisms.
Increased high-confidence human protein-chemical interactions by 45% over the previous version, reaching 367,000 interactions.
Restricted interspecies interaction score transfers exclusively to orthologous proteins, improving annotation precision across protein families.

Cite This Study

Kuhn et al. (2013) studied this question.

synapsesocial.com/papers/69d71bd7ef370a38abf5092b https://doi.org/10.1093/nar/gkt1207

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Implication

Database update reports an expanded network of protein-chemical interactions and user-data integration, highlighting enhanced functional annotation across diverse organisms.

STITCH 4: integration of protein–chemical interactions with user data

Discussion

Member takes

Implication

Key Points

Cite This Study

STITCH 4: integration of protein–chemical interactions with user data

Discussion

Member takes

Implication

Key Points

Cite This Study

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