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[bioontology-support] Help with Submission

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Mar 23 13:58:18 PDT 2016


Hello Ying Qin,

I downloaded and looked at the OWL file for your version 1.2 submission.  It looks like there are some syntax issues in the ontology the prevent BioPortal, and also the Protege ontology editing application from parsing / loading this ontology.  For example, trying to open your ontology in Protege results in the following error:


[cid:65AD45E6-03D6-45BB-8DBA-7A07ED7AEAE7 at stanford.edu]


On line 273 of your ontology there is some embedded HTML that seems to be causing the parsing errors:

<Definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Body composition defined most broadly refers to the proportions of fat mass (FM) and fat-free mass (FFM) or lean body mass (LBM) but also encompasses a related concept of regional body fatness. With an increase in FM or adiposity, there may be changes in the relative distribution of fat, for example, toward visceral or dorsal deposits and away from limb fat. Regional distribution of fat also changes normally with maturation and differentially between sexes; changes that may be aggravated by overweight or obesity. Early identification of patterns of regional fatness that may be associated with risky profiles is also encouraged. Scientific and practical guidance on which protocol may be best suited for a study’s needs are offered here: <a href="http://www.phenxtoolkit.org/toolkit_content/supplemental_info/anthropometrics/additional_info/Body_Composition_Guidance.doc">Body Composition Guidance</a> </Definition>

I noticed embedded HTML in other portions of your ontology, e.g., on line 303:

<Definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dominance is measured to assess the movement, mobility, and flexibility of an individual to determine which side of the body the study subject favors or the strength of hand activity.<strong><u></u></strong></Definition>

I will try to connect with one of the ontology experts on the Protege team either today or tomorrow to ask how embedded HTML should be formatted in order for ontology parsers to correctly handle it.  I’ll post again when I have more information for you.

Best,
Jennifer






On Mar 23, 2016, at 10:09 AM, Qin, Ying <yingqin at rti.org<mailto:yingqin at rti.org>> wrote:

Hi,

My name is Ying Qin, I am the contact person for the project “PhenX Phenotypic Terms<http://bioportal.bioontology.org/ontologies/PHENX>” on BioPortal (http://bioportal.bioontology.org/ontologies/PHENX ). I did a version 1.2 submission yesterday, but it seems like there is an error, the pagehttp://bioportal.bioontology.org/ontologies/PHENX?p=classes&conceptid=root doesn’t come up. Then I did another version 0.9 submission, this version was submitted 3 years ago and it was a successful submission. However, even for this version the page still doesn’t come up.

Can you please help? Please contact hpan at rti.org<mailto:hpan at rti.org> since I will be out of office for a few weeks.

Thank you!

~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Ying Qin
Research Computing Division
Research Triangle Institute
919-316-3473
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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