Great work Andra! Is there any possibility to add for Ensembl related properties (Gene ID, Transcript ID etc.) the version of Ensembl from which these Ids are extracted (maybe by adding a qualifier to the ID value) as Entrez seems to provide this information? Between Ensembl versions these IDs can change in some cases very drastically, so a gene can have a completely different ID or an ID can point to a different item in two Ensembl versions. Without knowing the Ensembl version number these IDs are not that useful especially when trying to correlate them with older published IDs.
Thanks, Günther
On Fri, 17 Oct 2014 23:29:20 +0200, Andra Waagmeester andra@micelio.be wrote:
The suggestion to use wbeditentity was great. It took me some time to
get
used to using that call, but finally I managed and the optimisation was great. So great that we also finished including the Mouse genome, yesterday. It only took 2 days to complete, in contrast to the weeks
with
the human genome. The suggestion to use wbeditentity really made my day.
Adding the mouse genome to wikidata, did however resulted in ~1000 duplicates. [1]
The issue is that an items already existed with an identical identifier
and
as such resulted in unique value violations [2]
In our current approach we can't prevent this, since the gene
description
is currently key. We are looking into ways to use the identifier as key
in
contrast to the label as we do now. The simplest option would be to add
the
identifier as alias, but it would be ideal if we could use the same algorithm as the one generating the constrained violations, before
adding a
new item. Is this possible? Can a bot query for a claim P351 with a
given
value (e.g. 1017).
Any input would be appreciated.
Regards,
Andra
[1]
https://www.wikidata.org/wiki/User_talk:Andrawaag#.7E_1000_duplicates .
[2] (
https://www.wikidata.org/wiki/Wikidata:Database_reports/Constraint_violation...
On Tue, Sep 30, 2014 at 9:05 PM, Daniel Kinzler <daniel.kinzler@wikimedia.de
wrote:
What makes it so slow?
Note that you can use wbeditentity to perform complex edits with a
single
api call. It's not as streight forward to use as, say, wbaddclaim, but much more powerfull and efficient.
-- daniel
Am 30.09.2014 19:00, schrieb Andra Waagmeester:
Hi All,
I have joined the development team of the ProteinBoxBot(https://www.wikidata.org/wiki/User:ProteinBoxBot) . Our goal is to make Wikidata the canonical resource for referencing and translating
identifiers for
genes and proteins from different species.
Currently adding all genes from the human genome and their related
identifiers
to Wikidata takes more then a month to complete. With the objective
to
add other
species, as well as having frequent updates for each of the genomes,
it
would be
convenient if we could increase this throughput.
Would it be accepted if we increase the throughput by running
multiple
instances
of ProteinBoxBot in parallel. If so, what would be an accepted number of parallel instances of a bot to run? We can run multiple instances
from
different
geographical locations if necessary.
Kind regards,
Andra
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Wikimedia Deutschland Gesellschaft zur Förderung Freien Wissens e.V.
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