Ontology name in OBO file

[vasiliy-bout]

While we were playing with OBO to OWL convertors we noticed that resulting OWL file contains a bunch of namespaces declared as the very beginning. For example, this is the head of uberon.owl file that we have created from uberon.obo manually (you can find OBO file here http://www.berkeleybop.org/ontologies/uberon/):

<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#"
     xml:base="http://purl.obolibrary.org/obo/uberon.owl"
     xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:core="http://purl.obolibrary.org/obo/uberon/core#"
     xmlns:core2="http://purl.obolibrary.org/obo/core#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:doap="http://usefulinc.com/ns/doap#"
     xmlns:terms="http://purl.org/dc/terms/"
     xmlns:obo="http://purl.obolibrary.org/obo/"
     xmlns:foaf="http://xmlns.com/foaf/0.1/"
     xmlns:dc="http://purl.org/dc/elements/1.1/">
    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon.owl">
        ...
    </owl:Ontology>
    ...
</rdf:RDF>

But when we convert cellosaurus.obo into cellosaurus.owl we get the following namespaces:

<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/TEMP#"
     xml:base="http://purl.obolibrary.org/obo/TEMP"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:TEMP="http://purl.obolibrary.org/obo/TEMP#"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/TEMP">
        ...
    </owl:Ontology>
    ...
</rdf:RDF>

And this TEMP looks very frustrating.

The reason why this TEMP occurs is that cellosaurus.obo has no ontology name specified. If you look into uberon.obo you will see this line:

ontology: uberon

So we added missing line to the cellosaurus.obo after the last subsetdef definition:

subsetdef: Telomerase_immortalized_cell_line "Telomerase immortalized cell line"
subsetdef: Transformed_cell_line "Transformed cell line"
subsetdef: Undefined_cell_line_type "Undefined cell line type"

ontology: cellosaurus

! Description: Cellosaurus: a controlled vocabulary of cell lines
! Geneva, Switzerland

And after that we get nice OWL file with the following namespaces:

<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/cellosaurus.owl#"
     xml:base="http://purl.obolibrary.org/obo/cellosaurus.owl"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:cellosaurus="http://purl.obolibrary.org/obo/cellosaurus#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cellosaurus.owl">
        ...
    </owl:Ontology>
    ...
</rdf:RDF>

So, please, add ontology: cellosaurus line to the OBO file.

[AmosBairoch]

ok, we will fix this for the next release.
Best
Amos

On 14.06.2016 21:32, Vasiliy Bout wrote:

While we were playing with OBO to OWL convertors we noticed that
resulting OWL file contains a bunch of namespaces declared as the very
beginning. For example, this is the head of |uberon.owl| file that we
have created from |uberon.obo| manually (you can find OBO file here
http://www.berkeleybop.org/ontologies/uberon/):

<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#"
xml:base="http://purl.obolibrary.org/obo/uberon.owl"
xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:core="http://purl.obolibrary.org/obo/uberon/core#"
xmlns:core2="http://purl.obolibrary.org/obo/core#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon.owl">
...
/owl:Ontology
...
/rdf:RDF

But when we convert |cellosaurus.obo| into |cellosaurus.owl| we get
the following namespaces:

<rdf:RDF xmlns="http://purl.obolibrary.org/obo/TEMP#"
xml:base="http://purl.obolibrary.org/obo/TEMP"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:TEMP="http://purl.obolibrary.org/obo/TEMP#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/TEMP">
...
/owl:Ontology
...
/rdf:RDF

And this |TEMP| looks very frustrating.

The reason why this |TEMP| occurs is that |cellosaurus.obo| has no
|ontology| name specified. If you look into |uberon.obo| you will see
this line:

|ontology: uberon |

So we added missing line to the cellosaurus.obo after the last
|subsetdef| definition:

|subsetdef: Telomerase_immortalized_cell_line "Telomerase immortalized
cell line" subsetdef: Transformed_cell_line "Transformed cell line"
subsetdef: Undefined_cell_line_type "Undefined cell line type"
ontology: cellosaurus ! Description: Cellosaurus: a controlled
vocabulary of cell lines ! Geneva, Switzerland |

And after that we get nice OWL file with the following namespaces:

<rdf:RDF xmlns="http://purl.obolibrary.org/obo/cellosaurus.owl#"
xml:base="http://purl.obolibrary.org/obo/cellosaurus.owl"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:cellosaurus="http://purl.obolibrary.org/obo/cellosaurus#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cellosaurus.owl">
...
/owl:Ontology
...
/rdf:RDF

So, please, add |ontology: cellosaurus| line to the OBO file.

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#3, or mute the
thread
https://github.com/notifications/unsubscribe/AIdEcnc-7RNjFd6wPz4qbaYcbRkfMCxAks5qLwHggaJpZM4I1raN.Web
Bug from
https://github.com/notifications/beacon/AIdEcrxi9b1XucRUpGKg_1z4TUg9eIAKks5qLwHggaJpZM4I1raN.gif

---

Professor and Director of the Dept. of Human Protein Sciences at the Faculty of Medicine of the University of Geneva
Group leader at the SIB - Swiss Institute of Bioinformatics

Preferred email: [email protected]

Alternative email: [email protected]