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11
2008
A New Presentation Regarding ChemMantis
Posted by: Antony Williams in ChemMantisCopyright©2008 Antony Williams
I’ve posted a new presentation regarding ChemSpider/ChemMantis on Slideshare. The first part is the usual ChemSpider intro stuff. For ChemMantis start at slide 39…
Note that we’ve now started expanding the handling of “Species” handling by adding specific dictionaries. We’ll be adding support for fungi, bacteria, viruses etc. See slide 75 for a screenshot.
Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry
View SlideShare presentation or Upload your own.
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November 13th, 2008 at 11:15 pm
A fairly-easy way to get lists of species names is to use the NCBI Taxonomy browser. Start here:
http://www.ncbi.nlm.nih.gov/
Select “Taxonomy” from the list of databases and enter e.g. “Bacteria”. Or, if you happened to know the NCBI taxid of your organisms (Bacteria = 2), you could enter “uid[2]“.
That will take you to a link for Bacteria: clicking the link will show a tree of bacterial genera. The page may take a while to load. If you enter “5″ in the display level, the page will reload (even more slowly) with species names.
You could parse the HTML for that page. Alternatively, taxonomy files are downloadable at the NCBI FTP site for use with your own scripts and databases.
November 14th, 2008 at 4:10 pm
Plants are poorly handled in NCBI taxonomy since so few have been examined genetically. NCBI is so rigorously oriented to genetics that for plants they use a gene based APG hierarchy, instead of the classic Chronquist system, which ends up tossing most plants into uncharacterized Misc.