Your Favorite Gene and NextBio
Your Favorite Gene(YFG)
Sigma-Aldrich’s Your Favorite Gene search engine is powered by Ingenuity’s Knowledge Base, one of the largest repository of biological and chemical networks which makes it an excellent exploratory tool. Initial search results can be further explored through dynamic networks rendered using Ingenuity’s Knowledge Base, offering deep insight into different types of interactions. In order to model and evaluate prospective experiments, user can search by gene, protein, function, disease, species, tissue or pathway to access a range of previous research findings and biological information. YFG not only helps to design effective experiment but it is also instrumental for a better selection of experimental products such as antibodies, bio-active molecules, bio-assays mostly offered by Sigma-Aldrich. YFG reporting interface is well structured and highly interactive. For example Interaction network and Canonical Pathway provides flash based network explorers
Cons: At first place you can not do anything else other than printing and exploring the results, for example YFG does not provide any options to save your analysis. Unless you have access to Ingenuity Pathways Analysis tool you can not export/import the analysis/experimental data. There is no API support for YFG which is very critical feature for process automation (LIMS perspective). Last but not least, experimental product offerings are totally restricted to Sigma-Aldrich’s portfolio.NextBio
Take all cons of YFG as pros of NextBio, for example NextBio has (I assumed API features are free to registered users)
- A REST-based search API to retrieve data out of NextBio
- An API for secure bulk import of data
- An auto-complete widget for search and tagging using our ontology
Now on search area, apart from searching for gene, protein, function, disease, species, tissue or pathway NextBio interface also provide information about clinical trials , public domain microarrays data, mutation and phenotypic studies. For example it helped me to locate the ongoing clinical trail studies associate with LDL receptor pathway. Further NextBio can be used as collaborative web 2.0 interface, which enables to connect with people working in your area of research. Another major feature is data and project sharing between users within the NextBio community.
Cons: Reporting interface is tabbed one, mostly text oriented. NextBio interface does not provide any visual exploration for the search results like YFG network explorer, but I guess that drawback can be compensated at user end using APIs with freely available tolls such as Graphviz, aiSee, Gaggle etc. As I mentioned YFG mostly feature experimental products from Sigma-Aldrich, but as of now there is no such utility with NextBio, which can be major improvement area in the future. For example NextBio can utilize/monetize its search interface to populate the related products from different vendors, it will allow users to design their experimental studies around available product options, very much like eMolecules.com which initially started as chemical molecule search engine and later transformed into e-commerce solution for chemical molecules. Both YFG and NextBio do not provide chemical structure search, they typically rely on the text based search.
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Guess what I need both for my curation setup
Your Favorite Gene and NextBio: In last few months I have tried several customized and/or vertical search engine.. http://tinyurl.com/coesx3
Thank you very much for the post!!
I also like the search-engine topic, but I didn’t know too much about science-related ones.
It is not very much related to science, but if you want to know more on search engines in general I recommend you this old good web site:
- http://www.searchlores.org/main.htm
Your Favorite Gene and NextBio- by Fisheye Perspective http://tinyurl.com/coesx3
reading “your favorite gene and nextbio” http://is.gd/r0IX from @abhishektiwari