There are about 47000 genes. In the first step the bot check if an entry already exists and, if not a new entry is made subsequently three claims are added (Entrez Gene ID (P351) https://www.wikidata.org/wiki/Property:P351#top found in taxon (P703) https://www.wikidata.org/wiki/Property:P703#top, subclass of (P279)) as well as synonyms. Currently this process takes a week to complete. In a second phase identifiers for each gene are obtained and added as respective claims. Typically this ranges from 1 claim per property to up to 20 claims per property (This is a rough estimate). This bot has been running for 2 weeks and is currently at 74% of all genes covered.
Currently each entity creation and subsequent claims are unique API calls. So using the wbeditentity will probably result in an improvement. Thanks for the suggestion.
Cheers, Andra
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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-- Daniel Kinzler Senior Software Developer
Wikimedia Deutschland Gesellschaft zur Förderung Freien Wissens e.V.
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