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[bioontology-support] [BioPortal] Feedback from Erika SALLET

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Jun 8 17:14:13 PDT 2021


Hello Erika,

On Jun 4, 2021, at 2:47 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Erika SALLET

Email: erika.sallet at inrae.fr<mailto:erika.sallet at inrae.fr>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FEDAM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fedamontology.org<http://252Fedamontology.org>%252Fformat_2572%26jump_to_nav%3Dtrue

Feedback:

Hello,
The direct link to get the BAM description looks broken : http://edamontology.org/format_2572

Could you be more specific about what you feel is broken? The URL you provided above (http://edamontology.org/format_2572) is the class ID for the BAM class. The BioPortal application is displaying the class information as it was declared in the ontology source file:

<!-- http://edamontology.org/format_2572 -->

<owl:Class rdf:about="http://edamontology.org/format_2572">
    <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
    <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
    <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
    <created_in>beta12orEarlier</created_in>
    <documentation rdf:resource="https://samtools.github.io/hts-specs/SAMv1.pdf"/>
    <oboInOwl:hasDbXref rdf:resource="https://samtools.github.io/hts-specs/SAMv1.pdf"/>
    <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>
    <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/edam#edam"/>
    <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/edam#formats"/>
    <rdfs:label>BAM</rdfs:label>
</owl:Class>


Kind regards,
Jennifer

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