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Questions tagged [ontology]

Ontologies are collections of terms organized in a graph that can be used to annotate biological data, for example, tagging genes or variants with terms from disease or phenotype ontologies. The most well known bio ontology is the Gene Ontology (GO), used for functional annotation of genes. Sites such as the OBO Foundry and Bioportal can be used to find bio-ontologies.

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Is there a way to measure cell similarity using python

I have a list of cell lines that should be compared against another list of cell lines as pairs. I am trying to find a way in order for me to compare two cells such as MCF7 and 10964c cell lines. I ...
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semantic similarity measurement for cell line ontologies

I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies. The problem I have is that I have found a Python library called Fastsemsim, but it ...
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What is the difference between a MeSH concept and a MeSH descriptor

Medical Subject Headings (MeSH) is a very comprehensive vocabulary to index the biomedical literature on Medline or PubMed (which is the major Biomedical literature database). MeSH is arranged into ...
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Why is Clostridium difficile toxin A + B outdated in snomed?

I'm looking at the new version of the Snomed dictionary and the concept 707993000 Clostridium difficile toxin A + B (substance) is deactivated (and outdated) since ...
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Quality checking benchmarks for clustering

I'm currently working with several RNAseq datasets from the ENCODE database. My approach to assessing the quality of the data, i.e, reproducibility is by automating the assessment of expression ...
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How can I create my own GO slim?

I know there are existing GO slims predefined. But does anyone know how I can create my own collection of GO terms for enrichment analysis?
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What's a good ontology for drug names?

I have ... A database with patient phenotypes in, stored as HPO terms Genetic data in whatever format I need I want ... To store drug names in a way that won't make my life difficult If it's ...
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Human body sites knowledge base

I'm looking for a lightweight knowledgebase describing the human body to annotate disease sites. I do not need a great level of detail, I just need a kind of basic organs/sub-organs taxonomy. I ...
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Mapping drug names to ATC codes

I'm interested working with the medication information provided by the UK Biobank. In order to get these into a usable form I would like to map them to ATC codes. Since many of the drugs listed in ...