Sample Charts for BioPAX

Each link below will direct this web app to load your user session with an available file of XML metadata depicting as an XHTML semantic net one of these sample contexts:

BioPAX level 2 - version 0.9, pulled from BioPAX.org site 6/6
HGH-HGHR assembly - from 6/3 hacking session, per Jeremy emai
HGH-HGHR merged - same as above, but merged with level 2 ontology

The above charts are ROUGH! My Java code is rough, as is my translations of the OWL files. But they nonetheless show BioPAX graphs being visualized and edited.

The RDF to XTM conversion is of interest. It uses these flawed mapping controls. If they were fixed up (takes new release), these samples would seem more elegant - and more like the other sample contexts in their :subject and :object handling.

Goals for this Toolkit Web App

The early charts above are useful to review despite their "warts", as they clarify work still needed to fully support BioPAX use cases. Fixing these problems soon and efficiently is just what this new on-line tool for charting formal graphs is meant to handle. Related solutions will significantly broaden the uses of BioPAX in real biotechnology applications..

Several of these use cases, in my estimate, would arise most simply from a shared pool of scripts in Java, JSPs, pHp, PERL, Scheme, Python, etc, all of which can offer BioPAX-focused services.using HTTP requests.

The scripts will manage and mutate formal graphs compliant with the rules of RDF, OWL, XTM and similar metadata standards. They will also seek to import and export such models in interchange formats, and any others deemed useful later.

The script base will form an open tool kit for processing pathway models, to be built and managed by the BioPAX community, representatives of which will commission them and license their use under a Community Source model. Ultimately, industrial subscribers pay usage fees that cover the centralized costs of building and enhancing infrastructure.

I am working on this site not as a Life Scientist, but as a contract Software Architect, who often works with ontologies and believes that BioPAX goals should be met with minimal limits and delay. My basic thesis is that significant executable software is required to do this, and that the sooner it gets built, the less time will be lost saving pennies instead of lives.

How to Help

Would your organization sponsor adding a copy of this toolkit web app to a new public site managed by the BioPathways Consortium, or some similar organization? It would let BioPAX supporters from all over post and swap utility scripts that simplify model perturbations, and/or use ontology-driven rules to help map into BioPAX any legacy file format.

Would you be willing to beta test this portable Java web app on your own intranet and/or PCs? If so, it will help train your own staff on semantic web transitions, boost their influence over initial tools in the BioPAX toolkit, and give them help from a new user community with synergistic goals.

Would you be willing and able, as an individual or as a group, to contribute time, expertise and/or working software to the instrastructure, or the shared pool of scripts, or to the administrative and organizational aspects of building and licensing such a web app?

In any of these case, please email me. We can jointly arrange that .

Thanks, Dan Corwin .

About those New Subtypes of Entity:

Topics and Associations are effectively sub-types of the BioPAX root concept, Entity. And Roles are just a generalization of PARTICIPANTS. They jointly comprise a new "upper ontology" layer that effectively explodes Entity into a small tree of replacement types, now defined formally under OntologyDesignPatterns

Check 'em out. They are pretty cool, and actually have man-centuries of production usage as ISO-standard design patterns. It is time BioPAX adopted them, because they make many tough modeling problems much simpler, yet remain compatibile with everything W3C has recommended for OWL-DL.