Question: Looking For Ontology Related To Biological Experiments
1
gravatar for Fred Fleche
8.4 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

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

biology ontology • 1.5k views
ADD COMMENTlink modified 11 days ago by rlwalls200810 • written 8.4 years ago by Fred Fleche4.3k
1

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

ADD REPLYlink written 8.4 years ago by Chris Evelo10.0k
5
gravatar for Pierre Lindenbaum
8.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

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 COMMENTlink modified 5 days ago by RamRS24k • written 8.4 years ago by Pierre Lindenbaum123k
1

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

ADD REPLYlink written 8.2 years ago by Fred Fleche4.3k
5
gravatar for Burke
8.4 years ago by
Burke270
Bethesda, MD
Burke270 wrote:

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 COMMENTlink written 8.4 years ago by Burke270
2
gravatar for Laurent
8.4 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

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

ADD COMMENTlink written 8.4 years ago by Laurent1.6k

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

ADD REPLYlink written 8.4 years ago by Fred Fleche4.3k
1
gravatar for rlwalls2008
11 days ago by
rlwalls200810
rlwalls200810 wrote:

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

ADD COMMENTlink written 11 days ago by rlwalls200810
0
gravatar for neelablore
3.2 years ago by
neelablore0
neelablore0 wrote:

http://www.projectsatbangalore.com/Bio.html

ADD COMMENTlink written 3.2 years ago by neelablore0
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