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[bioontology-support] Error on BioPortal Annotations (I think)

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Nov 28 14:12:00 PST 2016


Hi Luis,


On Nov 27, 2016, at 11:14 AM, Luís Campos <luis.filipe.lcampos at gmail.com<mailto:luis.filipe.lcampos at gmail.com>> wrote:

This term is supposed to be obsolete:

http://bioportal.bioontology.org/ontologies/RADLEX?p=classes&conceptid=http%3A%2F%2Fwww.radlex.org%2FRID%2F%23RID6096

But here it says it isn't obsolete:

http://data.bioontology.org/ontologies/RADLEX/classes/http%3A%2F%2Fwww.radlex.org%2FRID%2F%23RID6096

Only one of them can be right. :P


No, there doesn’t appear to be any errors with the BioPortal software here.  Rather, the problem is with the ontology source file.  BioPortal will only indicate that a class is obsolete if the ontology source file declares it as obsolete (i.e., owl:deprecated).  You can Google “owl deprecated” to read more about the topic of deprecation in OWL files.

I looked at the RadLex ontology.  The ontology authors created a class with a human readable label of “Obsolete Radlex Term”, and populated it with subclasses (including the class you mention above).  However, if you download the RadLex ontology source file and preform a search, there are no instances “deprecated" in the file.  In other words, they have not used the OWL language to formally declare any of the classes in this ontology as obsolete / deprecated.  The BioPortal user interface does not report this class as being obsolete if you select the class and look at the class details pane:


[cid:92AAC0F1-A9DA-4D2B-B087-4FC763A91F6A at stanford.edu]


It is simply displaying this class (RID6096) as a subclass of a class called “Obsolete Radlex Term”.  In contrast, here is a screenshot of a class from another ontology (ERO) where the class “primary cell culture” was formally declared as obsolete / deprecated in the ontology source file:


[cid:6C2BC156-B3AE-4EE0-8735-5D4D4C034969 at stanford.edu]


Notice the “Obsolete” row in the class details pane, which is set to true.  And, here is the snippet of syntax from that source file where the class is formally declared as obsolete (line with owl:deprecated is highlighted in bold):

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0001399">
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">primary cell culture</rdfs:label>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000009"/>
        <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#DeprecatedClass"/>
        <obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A culture of primary lymphocytes.</obo:IAO_0000112>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Any cell line that has yet to be passaged and/or a cell that has not been immortalized.</obo:IAO_0000115>
        <obo:IAO_0000231 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Decided category did not fit into improved cell line hierarchy implemented in sprinig 2014 for stem cell line modeling. Will migrate all data annotated to this class to more appropriate class in new hierarchy.</obo:IAO_0000231>
        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Matthew Brush</obo:IAO_0000117>
        <obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Matthew Brush</obo:IAO_0000119>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Placeholder for class to be imported from the Reagent Ontology (ReO).</rdfs:comment>
        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Primary cells</obo:IAO_0000118>
        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
    </owl:Class>


The BioPortal REST API also correctly indicates that this “primary cell culture” class is obsolete / deprecated:


[cid:BABD7C3C-5F03-4918-8D8D-08D69034CFDD at stanford.edu]


Hope that explanation helped.

Kind regards,
Jennifer


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