Looking For Ontology Related To Biological Experiments
5
1
Entering edit mode
11.2 years ago

Hello,

I am thinking about implementing a small/simple web application where scientists can share their protocols. I would like the scientist to be able to link their protocols to some tags like PCR, Western Blot, and so on so forth.

I would like to auto-suggest these tags. To do so I would like to use an already available set of tags.

So is there any ontology related to biological experiments that is already available. Or any good tips or suggestions are welcome.

Thanks in advance,

Fred

ontology biology • 2.1k views
ADD COMMENT
1
Entering edit mode

Did you check myexperiment.org? it might already do what you want to do.

ADD REPLY
5
Entering edit mode
11.2 years ago

see the information-artifact-ontology http://code.google.com/p/information-artifact-ontology an "ontology of information entities, originally driven by work by the OBI..."

The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of life-science and clinical investigations.

but it looks complicated to me.

You can also search for an ontology in the bioportal http://bioportal.bioontology.org

e.g: http://bioportal.bioontology.org/ontologies/45410

The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.

ADD COMMENT
1
Entering edit mode

I finally chose Pierre's response since I used the bioportal to find the ontology that fit my needs

ADD REPLY
5
Entering edit mode
11.2 years ago
Burke ▴ 290

The Ontology for Biomedical Investigations is what you are looking for. It is a well formed ontology that is part of the OBO Foundry is the place to start. It will ahve the controlled vocabularies that you seem to be looking for.

To match the terms from the protocols and the ontolgoy LingPipe alias-i.com/lingpipe/ has a great Jacquard similiarity implementation, if you are using Java that is.

ADD COMMENT
2
Entering edit mode
11.2 years ago
Laurent ★ 1.7k

The The Open Biological and Biomedical Ontologies might be a good start.

ADD COMMENT
1
Entering edit mode

Laurent thanks for this nice suggestion. Indeed the search text box is very useful to find out Ontologies to a given term.

ADD REPLY
1
Entering edit mode
2.8 years ago
rlwalls2008 ▴ 10

Another good resource for tagging is the EDAM ontology. https://www.ebi.ac.uk/ols/ontologies/edam

ADD COMMENT
0
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 2029 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6