Question: How Can I Learn More About Go Ontologies?
7
gravatar for Ethan Strauss
9.7 years ago by
Ethan Strauss70 wrote:

Hi, I would like to learn more about Gene Ontologies and the especially programmatic manipulation of ontologies. I have used GO for classifying genes in the past, but I have never really understood the structure of the ontologies. Any suggestions would be appreciated. Thanks, Ethan

gene programming • 2.0k views
ADD COMMENTlink modified 9.7 years ago by User 6659970 • written 9.7 years ago by Ethan Strauss70

Thaman, while the answers below are very interesting I wonder what it is you really want to do through "programmatic manipulation of ontologies".

ADD REPLYlink written 9.7 years ago by Chris Evelo10k

Ethan, while the answers below are very interesting I wonder what it is you really want to do through "programmatic manipulation of ontologies".

ADD REPLYlink written 9.7 years ago by Chris Evelo10k

i agree with chris - we need a specific example of what you want to achieve

ADD REPLYlink written 9.7 years ago by User 6659970
7
gravatar for User 6659
9.7 years ago by
User 6659970
User 6659970 wrote:

Hi Ethan

I haven't worked with computational ontologies for years but I might be able to give you some pointers to help you out. An ontology is just someone's specification of a particular domain - their world view. What you can say about the world or how you describe the world is limited by the computational languages available and the constructs within them for representing information. In other words your view of the world isn't a true world view- you are limited by the expressivity of the language. this used to be called the interaction problem in the old days but I'm sure they have a new name for it now.

So that said, people write biological ontologies in the different languages available and these languages will have different constructs for modelling information. If you are a programmer, a database design written in EER could be seen as on ontology, or UML diagrams are ontologies. They are a specification of a conceptualiztion after all! But common ontology languages have notions like is-a and has-a constructs e.g. a GPCR receptior IS-A protein which HAS-A transmembrance domain. There are also things like description logics and OWL and probably tonnes of other 'mark up' languages for representing the struture of information.

Programmatic manipulation of an ontology depends entirely on the specific ontology and the language it is written in. In other words the programmatic constructs for accessing the ontology will depend entirely on the inherent structure of the ontology. Most of them are ultimately big hierarchies like a traditional OO inheritance hierarchy

So that really is an answer to your question about the structure of ontologies. I can't be more specific about programmatic access without a specific ontology to talk about. If you look on the GO website there is a dizzying array of ontology tools. You might be better to ask some smaller specific questions about a specific ontology you don't understand.

ADD COMMENTlink modified 9.7 years ago • written 9.7 years ago by User 6659970
5
gravatar for Andra Waagmeester
9.7 years ago by
Maastricht, the Netherlands
Andra Waagmeester3.2k wrote:

http://www.geneontology.org/GO.contents.doc.shtml

A search google with "gene ontology api" resulted in: http://www.geneontology.org/GO.database.shtml

ADD COMMENTlink written 9.7 years ago by Andra Waagmeester3.2k
2
gravatar for Thaman
9.7 years ago by
Thaman3.3k
Finland
Thaman3.3k wrote:

In simple terms understanding structure of Gene ontology is all about comprehending the Schema of particular Ontology database. Schema of database gives us clear view of how information are stored, tables, fields and their relationship.

alt text

Schema Link

In above figure you can see some parts of database where there are tables, fields, attributes, relationship and along with primary ID. Now programming with the GeneOntology is all about knowing how information are stored and way of querying it in Ontology database.

MySql connection parameters for the GO database mirror at the EBI

Parameter   Value

host        mysql.ebi.ac.uk
user        go_select
password    amigo
database    go_latest
port        4085

Similarly you can manipulate ontology with perl, python, R, Ruby or whatever language you know if you go through documentation.

I strongly believe R is the best choice for programatic manipulation of GO, there are several Bioconductor packages like topGO, GOstats. Further excellent tutorial at Blue Collar Bioinformatics, R & Bioconductor Manual, GO related libraries and more teaching resources

Hope it helps

Edit - Previous Schema image updated!

ADD COMMENTlink modified 14 months ago by _r_am31k • written 9.7 years ago by Thaman3.3k

I am afraid this figure is misleading. It is not dealing with Gene Ontology. 'gene_product_homology' or gene_product_homolset is not part of GO definitions. Can you post original source or context of the the figure. Please let me know if I am missing something.

ADD REPLYlink written 9.7 years ago by Khader Shameer18k

I have just trim the figure from http://www.geneontology.org/images/diag-godb-er.jpg , If I am missing something please let me know

ADD REPLYlink modified 14 months ago by _r_am31k • written 9.7 years ago by Thaman3.3k

Thanks Thaman. You may give the link to full figure for more clarity.

ADD REPLYlink written 9.7 years ago by Khader Shameer18k

Ok I will do that

ADD REPLYlink written 9.7 years ago by Thaman3.3k
1
gravatar for Mary
9.7 years ago by
Mary11k
Boston MA area
Mary11k wrote:

The National Center for Biomedical Ontology may have some leads that are useful too:

http://www.bioontology.org/

Check out their "Dissemination & Training" links. One part is a 2-day course.

ADD COMMENTlink written 9.7 years ago by Mary11k
0
gravatar for Bert Overduin
9.7 years ago by
Bert Overduin3.7k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.7k wrote:

Please have a look here:

http://www.geneontology.org/GO.tools.shtml

and

http://www.geneontology.org/GO.tools.software-libraries.shtml

ADD COMMENTlink modified 14 months ago by _r_am31k • written 9.7 years ago by Bert Overduin3.7k
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