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Formats we'd like to add to the ontology

https://github.com/edamontology/edamontology/issues?q=is%3Aopen+is%3Aissue+author%3Ajonrkarr+no%3Amilestone

Contributing to the EDAM ontology

1. Install Git

2. Clone this Git repository

   git clone https://github.com/biosimulators/edamontology.git
   

3. Change to the directory for this repository

   cd edamontology
   

4. Enable Git hooks for this repository

   chmod +x .githooks/post-commit
   chmod +x .githooks/pre-commit
   git config core.hooksPath .githooks
   

5. Open the EDAM_dev.owl file in a text editor

6. Add a term for each modeling format before <!-- http://edamontology.org/operation_0004 --> (around line 37,000). Following the example below:

    <!-- http://edamontology.org/format_4019 -->
   
    <owl:Class rdf:about="http://edamontology.org/format_4019">
        <created_in>1.26</created_in>
        <rdfs:label>VCML</rdfs:label>
        <oboInOwl:hasExactSynonym>Virtual Cell Markup Language</oboInOwl:hasExactSynonym>
        <file_extension>xml</file_extension>
        <file_extension>vcml</file_extension>
        <media_type rdf:resource="http://www.iana.org/assignments/media-types/application/vcml+xml"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/edam#edam"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/edam#formats"/>
        <oboInOwl:hasDefinition>Format for models developed with the Virtual Cell biomodeling and simulation software suite.</oboInOwl:hasDefinition>
        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3241"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3869"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <documentation rdf:resource="https://vcell.org/support"/>
        <rdfs:seeAlso rdf:resource="https://en.wikipedia.org/wiki/Virtual_Cell"/>
        <example rdf:resource="https://vcell.org/vcell-published-models"/>
        <citation rdf:resource="http://doi.org/10.1049/iet-syb_20080102"/>
        <citation rdf:resource="http://doi.org/10.1093/bioinformatics/btt660"/>
        <repository rdf:resource="https://github.com/virtualcell/vcell/"/>
        <information_standard rdf:resource="https://co.mbine.org/standards/miriam"/>
        <ontology_used rdf:resource="http://www.ebi.ac.uk/sbo/"/>
        <ontology_used rdf:resource="http://biomodels.net/kisao"/>
        <organisation rdf:resource="https://health.uconn.edu/cell-analysis-modeling/"/>
    </owl:Class>

7. Commit changes

   git commit -m "Added term for XXX format"
   

8. Push changes

   git push