Posts Tagged ‘biology’

eXframe Platform Demos Power Of The Semantic Web For Biology

sccommonsA Drupal ++ platform for semantic web biomedical data – that’s how Sudeshna Das describes eXframe, a reusable framework for creating online repositories of genomics experiments. Das – who among other titles is affiliate faculty of the Harvard Stem Cell Institute – is one of the developers of eXframe, which leverages Stéphane Corlosquet’s RDF module for Drupal to produce, index (into an RDF store powered by the ARC2 PHP library) and publish semantic web data in the second generation version of the platform.

“We used the RDF modules to turn eXframe into a semantic web platform,” says Das. “That was key for us because it hid all the complexities of semantic technology.”

One instance of the platform today can be found in the repository for stem cell data as part of the Stem Cell Commons, the Harvard Stem Cell Institute’s community for stem cell bioinformatics. But Das notes the importance of the reusability aspect of the software platform to build genomics repositories that automatically produce Linked Data as well as a SPARQL endpoint, is that it becomes easy to build new repository instances with much less effort. Working off Drupal as its base, eXframe has been customized to support biomedical data and to integrate biomedical ontologies and knowledge bases.

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Making a Better Algorithm: Machine Learning & Biology

expertmaker

Michael Goldberg of Data Informed reports, “When Lars Hård, an artificial intelligence veteran, discusses developing a recommendation engine for a consumer product like perfume, he talks about harvesting many kinds of data. Product data. Consumer search engine data. Design data having to do with colors that men or women prefer. Pricing data. To Hård, founder and chief technology officer at Expertmaker, data in all its structured and unstructured forms represents signals that machine learning systems pick up to refine results for future interactions. The data, and those interactions, also figure into Hård’s work of applying principles of evolutionary biology to both business use cases, like shopping assistants, and medical research.” Read more

RDF and Mind Maps

Kerstin Forsberg has written an article about mind maps and how the concept of mapping the mind calls for RDF triples and formal models. She writes, “When I see these mind maps I see graphs just begging for RDF triples (subject, predicate, object)…  An interesting exercise would be to have the Parkinson’s disease example completed in the concept mapping tool (CMAP) the whole way down to SDTM. And export the mind maps using as RDF triples.”

She goes on, “When I these mind maps I can also see how easy it is to start drawing such diagrams and exporting them as representations of generic mind maps. Read more

Metaome Helps Bench Biologists Get More Value From Linked Data

How to help the bench biologist get value out of the wealth of life sciences Linked Data sets? Startup Metaome Science Informatics proposes to offer some help with its DistilBio semantic search and data integration technology, by streamlining the approach to posing user queries. The Distil in DistilBio stands for Data Integration using Semantic Technologies in the Life Sciences.

Metaome, which was founded by CEO Kalpana Krishnaswami and CTO Ramkumar Nandakumar as a bioinformatics services provider before transitioning to a product vendor, contains a few more than a dozen life sciences public data sets so far. Infomaticians in the life sciences space have the expertise to query such data across sets via SPARQL, but the front-line biologist isn’t necessarily an infomatician. So, DistilBio has created a query interface that makes it easier for them to ask large and complex questions in a simplified way across data sets while building a graph in the process.

“How does a user say what are the drugs used for Alzheimer’s disease and do have they have certain protein targets and are those protein targets implicated in other diseases?” says Krishnaswami. “To ask that in one shot right now is hard without working through a SPARQL endpoint using all the SPARQL syntax.”

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