#670 QC: Check for missing evidence before allowing submission

[Valerie Wood]

Canto should not allow sessions to be submitted if there is missing evidence.

The original ticket mentioned missing alleles, but that won't be able to happen after the multi-allele phenotype code is finished.

---

Old summary:

I wasn't sure that all of the incomplete info in the curation sessions was reported in the logs.
For instance this paper :
http://curation.pombase.org/pombe/curs/1cc5c597f8a24352
has missing evidence and allele, but no errors reported. Could you take a look?

[Kim Rutherford]

Currently the loader doesn't do very much checking. It assumes that if a session has been approved then it must be OK.

I'll add some checks.

[Kim Rutherford]

The missing evidence is reported already:
http://curation.pombase.org/dumps/pombase-build-2013-11-11-v1-l1/logs/log.2013-11-13-00-48-19.curation-tool-data-load-output

"error in 1cc5c597f8a24352: no evidence code for phenotype"

[Valerie Wood]

It might be best to do these checks at the Chado stage?

report if alleles or evidence are missing and prevent the session from being approved. That would save time for us going back and take the burden off the log checker person.

(although we should probably have both in case any slip through into chado from external files?)

[Valerie Wood]

might be best at the canto stage?

Report if evidences and alleles are missing when a session is approved
(it currently reports if conditions are not in the condition ontology)

On 13/11/2013 21:31, Kim Rutherford wrote:

Currently the loader doesn't do very much checking. It assumes that if
a session has been approved then it must be OK.

I'll add some checks.

---

[chado:#267] http://sourceforge.net/p/pombase/chado/267/ possible
problems not making it into log files

Status: open
Created: Wed Nov 13, 2013 03:05 PM UTC by Valerie Wood
Last Updated: Wed Nov 13, 2013 03:05 PM UTC
Owner: nobody

I wasn't sure that all of the incomplete info in the curation sessions
was reported in the logs.
For instance this paper :
http://curation.pombase.org/pombe/curs/1cc5c597f8a24352
has missing evidence and allele, but no errors reported. Could you
take a look?

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/pombase/chado/267/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

[Kim Rutherford]

Ticket moved from /p/pombase/chado/267/

[Valerie Wood]

Is this still relevant ?
Is it possible to have a canto annotation with no evidence?