BRO request

[Melissa Haendel]

Hi all,

So the eagle-i team is working on releasing our first annotation tool, and are looking to use a few parts of OBI and BRO for this first phase. 

In particular, we are hoping to use the BRO software branch. (When get to the OBI request we'll post them there and cc the resource-representation group as well). This email is specifically a request for changes to the BRO software branch. In particular, we would like to request that the multiple inheritance be fixed for the following terms:

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Approximate_Graph_Alignment Approximate Graph Alignment

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Computational_Geometry Computational Geometry

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Convolution Convolution

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Mining_and_Inference Data Mining and Inference

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Fast_Fourier_Transform Fast Fourier Transform

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Model_with_Closed_Form_Solutions Model with Closed Form Solutions

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Portal Portal

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Portlet_Component Portlet Component

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Searching_Sorting_and_Indexing Searching Sorting and Indexing

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Signal_Processing Signal Processing

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Signaling_Network_Reconstruction Signaling Network Reconstruction

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Text_Mining Text Mining

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Toolkit Toolkit

http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Workbench Workbench

Some of these have explicit relations where they may not be needed, but most likely represent multiple classes or non-disjoint parents. Obviously, defining terms in BRO will be very helpful in this regard (especially if multiple inheritance is required), but also time consuming. I know that some of you are using BRO and it may be that changes to these terms will result in data inconsistency. In the short term, we can just not use the terms where these changes might have effects on others. However, in the longer term, I'd argue that if we want BRO to be useful to more people and promote interoperability, then we should find a mechanism to reconcile these types of changes to the ontology for existing users. In any case, I just wanted to make a request for these terms to specifically get fixed, but also reach out to existing users to begin to understand each other's needs.

Many cheers,

and happy holidays to you all.

Melissa

Dr. Melissa Haendel

Lead Curator 
eagle-i Networking Research Resources
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[Trish Whetzel]

Hi Melissa,

I have been reviewing these terms and comparing the file that you sent yesterday with proposed locations of these terms in the hierarchy. However, some of the changes in that file re-locate the term to a different parent than what is currently stated in BRO. Do you have documentation on reasons for these proposed changes? For example for the term Portal.

Also, many of these terms do have definitions and will be added into the next release of BRO. If anyone is interested to help generate definitions for the remaining terms I would be more than happy to work on these together. 

Thanks,
Trish

[Melissa Haendel]

Hi Trish,

My specific request is that the multiple inheritance be corrected. The file I sent you was a rearranged BRO software hierarchy that we are using temporarily for our annotation tool. We will update our tool once BRO has been updated. 

That said, the rearrangements I put into our tool were to remove the multiple inheritance, cull some of the terms that we didn't think we'd need for now, and move some terms that I thought we would need or represented concepts that were better represented in other parts of the hierarchy. I did this all without definitions, so you should of course take it all with many grains of salt. 

I would just use what you see as suggestions that these terms should be looked at and defined, but not necessarily that they are in a correct position or have the best names. In the obo file, I did keep track of synonyms so you can see what was renamed.

cheers,

Melissa