🎁 10 Flagship events
We sponsored ISMB/ECCB 2025 in Liverpool and ran a UK track co-chaired by Carole Goble and Janet Thornton.
🔗 elixiruknode.org/news/2025/is...
#ISMBECCB #community
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Hashtag
#ISMBECCB
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If you are at the #ismbeccb in Liverpool, then don’t miss chatting with our Magdalena Schüttler, who will be presenting a poster on "Left Ventricular and Papillary Muscle Hypertrophy as Cardiac Markers for Fabry Disease" (poster B-489 in the TransMed track, today at 10:00-11:20 and 16:00-16:40)
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Graphic promoting the Earlham Institute heading to ISMB ECCB on 21-24 July 2025.
At #ISMBECCB2025 next week, scientists will be presenting the latest from the Earlham Institute covering #singlecell and #spatial workflows, #FAIRdata management, #longread sequencing and metagenomics, and #RNA biology.
#ISMBECCB #ISMB #ECCB #singlecell
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The workshop brought together researchers from academia and industry to brainstorm ideas for the next edition of the Health Privacy Challenge. 🤝
What’s next for the Health Privacy Challenge?
It will feature a dedicated session at CAMDA during ISMB/ECCB 2025 in Liverpool!
#ELSAAI #ISMBECCB
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Our bioinformaticians will be attending #ISMBECCB2025!
Catch our talks and posters on @expressionatlas.bsky.social,
@bioconductor.bsky.social, and Persist-seq
#ISMBECCB #ISMB #ECCB #singlecell
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From the TransMed COSI Organizing Committee:
Don’t forget to submit your abstracts for a talk or poster for the TransMed COSI track at #ISMBECCB 2025 on Tuesday, 22 July in Liverpool, UK!
🗓️ Deadline: 17 April
📥Submit here: www.iscb.org/ismbeccb2025/call-for-su...
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My slides from @bioontologies #ISMBECCB on the Ontology Development Kit are up: www.slideshare.net/cmungall/ontology-develo... - thanks to @micheldumontier and the other organizers for a great meeting!
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Inspired by #SMBE2020 / #ISMBECCB and looking for #Postdoc job? Develop your #bioinformatics & comparative #genomics skills & apply them to understanding function & evolution of #insect immunity. Uni. Lausanne & Swiss Institute of Bioinformatics. Details https://rmwaterhouse.org/jobs
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Gene set enrichment can be done with PubMed publications as signatures, Christian von Mering at the #ISMBECCB NetBio COSI
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Attending #ISMBECCB #ISMBECCB19 #ISMB19 #ISMBECCB2019 #ISMB2019? Visit us at poster #M32 to find out what @emblebi @complexportal can do for you and meet our new team member Kalpana!
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DR: Use existing RE tools: miRTex, miRIaD, Dexter. Ontologies/vocabs used: NCBI Gene, DO, GO, miRBase, BRENDA for loca. Parsing: Stanford coreNLP, BLIP Parser #ismbeccb
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DR: other relations extracted: miRNA as therapeutic target, relationship to survival rates, etc. #ismbeccb
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Debarati Roychowdhury: text mining knowledge maps for miRNAs. NER and Relation Extraction (RE) such as miRNA to (dys)regulated gene, miRNA to disease. #ismbeccb
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Peipei Ping: A reference set of curated biomedical data and metadata from clinical case reports. https://www.ncbi.nlm.nih.gov/pubmed/30457569 #ismbeccb
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Peipei Ping: Use embedded knolwedge graphs to predict similar patients, make predictions. #ismbeccb
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Peipei Ping: Bio-KARE uses 3 kinds of knowledge graphs. case graphs (individual patient in one CCR), instance graphs (aggregated over multiple patients), concept graphs (i.e ontologies). Use graph embedding to transfer to unified latent space #ismbeccb
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Peipei Ping: Bio-KARE: combines NER and relationship extraction, makes use of existing biomedical knowledgebases and ontologies. Uses transfer & reinforcement & imitation learning. #ismbeccb
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Peipei Ping: Bio-KARE: Knowledge Architecture and Relationship Enrichment. connects entities and relationships over multiple time frames #ismbeccb
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Peipei Ping: Learning from Clinical Case Reports (CCRs). >2m CCRs published. CCRs often contain temporal info reflecting dynamic nature of pathogenesis, but this is in text and not computable #ismbeccb
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JS: RGD PhenoMiner for quantitative phenotypes. Uses Clinical Measurement Ontology, Measurement Method Ontology, Environment Condition Ontology, Rat Strain Ontology #ismbeccb
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JS: OntoMate leverages structure in ontologies, and entire orthology group. Helps suggests new papers to curate. #ismbeccb
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JS: OntoMate enhances manual curation workflows, doesn't replace. Integrated into RGD literature curation UI. #ismbeccb
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Jennifer Smith: OntoMate - text mining over multiple species in @ratgenome database, performs NER over multiple different ontologies (GO, phenotype, others) #ismbeccb
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MP: using literature community networks to predicate gene-disease-chemical links. #ismbeccb
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MP: validation by enrich communities against mSigDb gene set database [hmm, could reflect shared bias...] #ismbeccb
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MP: building literature 'communities' through co-occurrence of MESH terms, clustering using recursive louvain algorithm #ismbeccb
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Minh Pham: combining manual curation and text mining to discover disease & drug specific pathways. #ismbeccb
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RD: PRETA method: disease-gene associations from OMIM, mine OMIM description for tissue mentions. use barcode (this one? http://barcode.luhs.org/ to check gene-tissue link in triangle is recapitulated #ismbeccb
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Ruth Dannenfelser: PRETA: predictions of disease-tissue associations (e.g. obesity-adipose tissue) #TextMiningCOSI #ismbeccb
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Oops, official hashtag is #ISMBECCB. Sorry for the repost
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