@rhea-db
Rhea is an expert curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI, and the reference for annotation of enzyme chemistry in UniProt. website: https://www.rhea-db.org SPARQL endpoint: https://sparql.rhea-db.org/sparql
The first release of 2026 of the Rhea database is out! Release 140 (2026-01-28) contains 18,343 unique reactions and 15,125 unique reaction participants, with 25M protein sequence entries annotated with Rhea reactions in UniProtKB.
Great work and an ingenious application of the UniProt and @rhea-db.bsky.social knowledgebases!
Very nice preprint on the importance of #FAIR data resources in the life sciences, for AI and generally for science, by a great @sib.swiss team led by @dessimoz.bsky.social. With @bgee.org inside ;)
zenodo.org/records/1572...
Speak up to prevent a major loss for the field. CASP, which helped shaping structural biology including AlphaFold is on the verge of shutting down. NIH funding has lapsed, UC Davis support ends and the core team is being let go. Painfully shortsighted.
A science fair of cancelled grants. The research that will be represented at this event (Tuesday) ranges from neuroscience, to astrophysics, to STEM education. The awarding agencies of the now-canceled grants include the EPA, DHS, NIH, NSF, USAID, and DOD. Open to the public.
Latest paper from the de Crecy lab is out!
A finding that answers a ~40 year old question: a eukaryotic high-specificity transporter for Q/q
This is a must-read piece by @math-rachel.bsky.social about AI evaluation, and how the system of reward and apportioning credit in AI research is broken rachel.fast.ai/posts/2025-0.... TL;DR -- we need deep fact checkers!
Got a #knowledgegraph want some use cases and example queries and how to share them: Read our paper in GigaScience https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf045/8133871?searchresult=1 Join us in #SPARQLing your #SPARQL to improve your #SPARQL ;)
Nice! As Metaboverse uses ChEBI, have you considered using Rhea or Rhea annotations from UniProt too?
This year's International Workshop on Open Molecular Informatics (IWOMI) (12.-16.05.25) will focus on the curation of open molecular data using multimodal large language models (LLM). If you are interested, please register at www.iwomi.net
[BC]Β² Basel Computational Biology Conference 2025 will take place on 8-10 September. The conference brings together over 500 international scientists from academia, industry, and healthcare to explore advancements at the intersection of #bioinformatics and artificial intelligence. See bc2.ch
New pathway "Mitochondrial carrier deficiency associated with shuttle disturbances (WP5507)" https://www.wikipathways.org/pathways/WP5507 "Reflecting the pathway as shown in Figure 43.2 of Blau et al. "Physicianβs guide to the diagnosis, treatment, and follow-up of inherited metabolic diseases"
New pathway "GIP and GLP-1 function by tissue (WP5509)" https://www.wikipathways.org/pathways/WP5509 "Functions of GIP and GLP-1, two agonists of which are found in the weight-loss drug tirzepatide (a.k.a. Mounjaro). "Pancreatic and exopancreatic function of glucoseβdependent insulinotropic polypepide (GIP) and glucagonβlike peptide (GLP)β1. GIP acts directly on the endocrine pancreas, bone, fat, gastrointestinal (GI) tract and brain. GLPβ1 acts directly on the endocrine pancreas, gastrointestinal tract, heart and brain." From Figure 2 in https://pmc.ncbi.nlm.nih.gov/articles/PMC4020673/."
New pathway: "Vedolizumab therapy for irritable bowel syndrome (WP5512)" https://www.wikipathways.org/pathways/WP5512 "Vedolizumab is a humanized monoclonal antibody with a predominantly gastrointestinal effect. It specifically inhibits leucocyte integrin Ξ±4Ξ²7, thus preventing its interaction with mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1), which is involved in the migration of lymphocytes from the blood stream to the intestinal tissue. Vedolizumab is indicated in the treatment of moderate to severe active Crohn's disease and ulcerative colitis in adult patients with poor response, loss of response, or intolerance to conventional treatment or to tumour necrosis factor alpha (TNF-Ξ±) antagonists." Inspired by Figure 1 in https://pubmed.ncbi.nlm.nih.gov/31470005/. Vedolizumab is also known by its trade name, Entyvio.
New pathway: "NSAIDs mechanism of action (WP5513)" https://www.wikipathways.org/pathways/WP5513 "Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit the cyclooxygenase isoenzymes COX1 and COX2 with varying degrees of specificity for the COX2 isoform. As a result, the conversion of arachidonic acid to prostaglandins (PGs) is inhibited. The main effects of PGs throughout the body are listed." Inspired by Figure 1 in PMID:32322101.
Februari 2025 WikiPathways update: 313 edits by 10 contributors and 4 new pathways in the last month. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://www.wikipathways.org/download.html
#biology #bioinformatics #openscience
Next BioSB @biosb.bsky.social HotTopics meeting: BioSB HotTopics meeting on Data representation of small molecules and their application March 25 in Amsterdam www.dtls.nl/data-represe... with Daniel Probst @skepteis.bsky.social, Gerard van Westen @gjpvwesten.bsky.social, and Gabriel Vogel
Out now, release 137 of Rhea featuring 17,422 reactions and 14,335 unique compounds from 18,284 publications. Rhea is used to annotate over 28 million proteins in UniProt (see www.uniprot.org/uniprotkb?qu...).
hi Egon! nice to see you
