Name: amidemos
Owner: The ContentMine
Description: null
Created: 2016-09-19 13:05:12.0
Updated: 2016-09-19 13:11:28.0
Pushed: 2017-09-29 10:07:44.0
Homepage: null
Size: 2051
Language: HTML
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These are a few demos of what the AMI tools can create for searching EuPMC.
Most projects were created with one-word searches using getpapers on EuPMC to create a CProject with the name as the term. Then the
cProject was normalized and the facets extracted in a single step.
apers -q aardvark -o aardvark -x -p
queries EuPMC for aardvark and creates a cProject aardvark. Then cmine is run with a default set of bioscience dictionaries.
e aardvark
which creates the snippets files and a summary in full.dataTables.html.
The snippets (facts) are linked to hypothetical Wikipedia articles (e.g. from aardvark we create the link<a href="http://en.wikipedia.org/wiki/Aardvark">Aardvark</a>). In some cases the item is not in Wikipedia and gives a “not found” page, but a surprisingly high percentage are. The use of wikidata will be a major enhancement.
We are now converting our bioscience dictionaries to have Wikidata ids. This will mean that e can create links only when there is a Wikidata ID and there is guaranteed to be a link to the Wikipedia page. We have about 15 current dictionaries and will re-run the analysis shortly
The tables are created with columns corresponding to:
The display uses the DataTables JS package enhancement which adds table management (e.g. chunking the display, search etc.). This library is automatically downloaded from the web. It won't display directly from the github site. Without the DataTables the display is a well-formed HTML table, just not interactive, so to get the full feel download the table and display it in your browser.
We retrieve all papers in EuPMC about Aardvarks, using the common name.
apers -q aardvark -o aardvark -x -p
This creates a cProject in a directory called aardvark
The command
e aardvark
will then run the default norma ami commands
we display the tables in browser as:
https://rawgit.com/ContentMine/amidemos/master/aardvark/full.dataTables.html
and downloadable as https://github.com/ContentMine/amidemos/master/aardvark/full.dataTables.html
We have done the same for “Zika” with a slightly different set of columns
apers -q zika -o zika -x -p
https://rawgit.com/ContentMine/amidemos/master/zika/full.dataTables.html
Carvone ( a terpene in caraway ) https://rawgit.com/ContentMine/amidemos/master/carvone/full.dataTables.html
Much of the procedure and vackground is given in presentations such as http://www.slideshare.net/petermurrayrust/high-throughput-mining-of-the-plantscience-literature which illustrates Carvone and describes the role of Wikidata.