Existing Ontology/Ies For Capturing Next Generation Sequencing Data And/Or Metadata

Question

[Abhi]

Hi All

Just wondering if there are any existing ontologies(I wud guess there might be few) which capture the meta-data / data in next generation sequencing analysis /experiment. We are trying to store data/meta-data about NGS projects locally and rather than developing some controlled vocabulary of our own I was wondering if we could use something which is already out there.

Thanks! -Abhi

Answer 1

[Pierre Lindenbaum]

try the EDAM ontology: http://edamontology.org/page#Download

$ curl -s "http://edamontology.org/EDAM.owl" | grep -i -A 10 -B 2 BAM 

    <owl:Class rdf:about="&lt;a href=" http:="" edamontology.org="" format_2572"="" rel="nofollow">http://edamontology.org/format_2572">
        <rdfs:label>BAM</rdfs:label>
        <rdfs:subClassOf rdf:resource="&lt;a href=" http:="" edamontology.org="" format_1921"="" rel="nofollow">http://edamontology.org/format_1921"/>
        <rdfs:subClassOf rdf:resource="&lt;a href=" http:="" edamontology.org="" format_2057"="" rel="nofollow">http://edamontology.org/format_2057"/>
        <rdfs:subClassOf rdf:resource="&lt;a href=" http:="" edamontology.org="" format_2333"="" rel="nofollow">http://edamontology.org/format_2333"/>
        <oboInOwl:hasDefinition>BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.</oboInOwl:hasDefinition>
        <created_in>beta12orEarlier</created_in>
        <oboOther:namespace>format</oboOther:namespace>
        <oboInOwl:inSubset>formats</oboInOwl:inSubset>
        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
        <oboInOwl:inSubset>bioinformatics</oboInOwl:inSubset>
        <oboInOwl:hasDbXref rdf:resource="&lt;a href=" http:="" samtools.sourceforge.net="" SAM-1.3.pdf"="" rel="nofollow">http://samtools.sourceforge.net/SAM-1.3.pdf"/>
        <documentation rdf:resource="&lt;a href=" http:="" samtools.sourceforge.net="" SAM-1.3.pdf"="" rel="nofollow">http://samtools.sourceforge.net/SAM-1.3.pdf"/>
    </owl:Class>

Answer 2

[sturm.marc]

There is also an ontology for NGS QC terms (see http://code.google.com/p/qcml/source/browse/trunk/cv/qc-cv.obo) which is part of the qcML project (http://code.google.com/p/qcml/).