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[bioontology-support] Advice needed for ontology social quality assessment research

Clement Jonquet jonquet at lirmm.fr
Wed Feb 24 16:50:24 PST 2016


Hi Melinda, 

 

Interesting research for sure. 

It would be interesting to know your metrics/criteria (size, metadata, coverage for given corpus, etc.) before assessing anything about the results. 

 

We have been working on recommending/selecting ontologies with Marcos (CC) and it depends a lot on what are the purpose and what are the criteria to serve those purposes.

 

The browse page offers different ordering (top right)

 <http://bioportal.bioontology.org/ontologies> http://bioportal.bioontology.org/ontologies 

This are also based on different criterias.

 

Clement

 

De : bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] De la part de Melinda Hardy McDaniel
Envoyé : samedi 13 février 2016 15:11
À : bioontology-support at lists.stanford.edu
Objet : [bioontology-support] Advice needed for ontology social quality assessment research

 

I am working on research regarding ontology quality evaluation from the viewpoint of its domain community. I am trying to assess the relative value of the ontologies in a community to the community’s members using metrics I have developed. I am testing my metrics using the BioPortal library because of its active community.

 

The results I obtained look very promising in that the highest ranked ontologies do seem to be the ones that are most used, but I am not sure whether the lowest ranked ontologies using my system are actually less well regarded.

 

Can you please take a look at the table I have below, which shows a subset of the results? If you are familiar with any of the ontologies listed can you please tell me whether these numbers appear correct? ( I also have rankings by keyword if that would be more easy to understand.)

 

Any other suggestions you can make or any other questions you may have would be extremely helpful to me.

Thanks very much in advance!

Melinda

10 Highest Ranked BioPortal ontologies 


Abbrev.

Name


 GO

Gene Ontology


 HP

Human Phenotype Ontology


 MIRO

Mosquito Insecticide Resistance Ontology


 MS

Mass Spectrometry Ontology


 SBO

Systems Biology Ontology


 MAT

Minimal Anatomical Ontology


 SO

Sequence Types and Features Ontology


 DOID

Human Disease Ontology


 MP

Mammalian Phenotype Ontology


 PTO

Plant Trait Ontology

 

10 Lowest Ranked BioPortal ontologies


Abbrev.

Name


 ONTOMA

Ontology of Alternative Medicine, French <http://bioportal.bioontology.org/ontologies/ONTOMA> 


ONTOPNEUMO

Ontology of Pneumology <http://bioportal.bioontology.org/ontologies/ONTOPNEUMO> 


 OntoVIP

Medical image simulation <http://bioportal.bioontology.org/ontologies/OntoVIP> 


 PVONTO

Pharmacovigilance Ontology <http://bioportal.bioontology.org/ontologies/PVONTO> 


 RCTONT

Randomized Controlled Trials Ontology <http://bioportal.bioontology.org/ontologies/RCTONT> 


 RNPRIO

Research Network and Patient Registry Inventory Ontology <http://bioportal.bioontology.org/ontologies/RNPRIO> 


 ROLEO

Role Ontology <http://bioportal.bioontology.org/ontologies/ROLEO> 


 suicideo

Traditional Medicine Meridian Value Sets <http://bioportal.bioontology.org/ontologies/TM-MER> 


 TM-CONST

Units Ontology <http://bioportal.bioontology.org/ontologies/UNITSONT> 


 TM-MER

 <http://bioportal.bioontology.org/ontologies/VSO> Vital Sign Ontology

 

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~
Melinda McDaniel
Doctoral Candidate

Computer Science Department
Georgia State University
Atlanta, GA 30302

 

 

 

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