Closed rcurrie closed 5 years ago
Or...
chr13:g.32363367:C>G
[{'pmid': 22962691,
'points': 40,
'snippets': [', in the BRCA2 gene, besides the exon 7 mutations described '
'above, only one mutation in exon 3, c.231T>G (p.Thr77Thr),16 '
'and two mutations in exon 18,<<< c.8165C>G>>> (p.Thr2722Arg)28 '
'and c.7992T>A (p.Ile2664Ile),16 have been reported to induce '
'exon skipping by altering splicing regulatory elements.',
'BRCA2<<< T2722R>>> is a deleterious allele that causes exon '
'skipping.',
'CA2 gene, besides the exon 7 mutations described above, only '
'one mutation in exon 3, c.231T>G (p.Thr77Thr),16 and two '
'mutations in exon 18, c.8165C>G <<<(p.Thr2722Arg>>>)28 and '
'c.7992T>A (p.Ile2664Ile),16 have been reported to induce exon '
'skipping by altering splicing regulatory elements.']},
There's also a new 'date' field in ISO format indicating the day the crawl happened:
{
"date": "2018-11-14T12:00:00-0800",
"papers": ...
"variants": ...
}
I've generated a preliminary literature.json using the same set of papers we downloaded for the current production but with the new matching and points:
3615 Papers and 9783 Variants vs. 2227 Papers and 3754 Variants currently in production
I have a bit more cleanup to do but then I'm going to do a new crawl to add papers from 11/14 till now so that once we settle on a new format we can use the latest papers as well.
Awesome!
On Wed, Feb 27, 2019 at 4:21 PM Rob Currie notifications@github.com wrote:
I've generated a preliminary literature.json http://public.gi.ucsc.edu/~rcurrie/literature-2019-02-27.json using the same set of papers we downloaded for the current production but with the new matching and points:
3615 Papers and 9783 Variants vs. 2227 Papers and 3754 Variants currently in production
I have a bit more cleanup to do but then I'm going to do a new crawl to add papers from 11/14 till now so that once we settle on a new format we can use the latest papers as well.
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Ran an updated crawl for all PMIDs as of yesterday with BRCA in the title or abstract:
17459 vs. 16980 PMIDs attempted (479 papers since last crawl on 11/18)
14520 (83%) vs. 14088 (83%) succeeded
3701 Papers and 9886 Variants exported (86 papers that were able to be downloaded and variants found since 11/18)
@zfisch New crawl with papers as of yesterday in the new format (last one above with full dictionary per variant) is here
Pull request on brcaexchange to handle new data and sorting at https://github.com/BRCAChallenge/brca-exchange/pull/1016 👍
The current literature.json uses a dictionary by pmid of snippets per variant:
Which does not allow for the papers to be ordered by quality of hit. Two general options are to switch to a list of tuples sorted by points of (pmid, points, list of top 3 snippets for this paper):
or a list of dictionaries with points where you'd need to sort and show based on points:
@falquaddoomi @zfisch Let me know which you'd prefer - no massive rush as I have some additional validation on the results to do.