Missing highlights for most relations

[JTFouquier]

I'm making this a running list of highlight errors to be debugged (low priority) as time allows. Consider editing the comment when each example is addressed.

Just one example... this is low priority because it is happening very rarely, but the blue/disease is not appearing. Might want to check the Pubtator.

[JTFouquier]

Example 2: Only "deficiency" was highlighted when NGLY1 should be highlighted.

[x0xMaximus]

• Disease is now appearing for 1539
• NGLY1 is still not included in highlight for 1434, are we sure on the the data intends NGLY1 is supposed to be highlighted?

[x0xMaximus]

How are we going to proceed with these? This type of an issue is dependent on pubtator and it's impossible now for QA user to evaluate if these are a data source problem or a YPet high lighting problem. I suggest we need to come to an agreement for determining what are words that are expected to be highlighted, this could be a new UI list or some way for QA user to differenciate between the two

[JTFouquier]

I'm sure you are aware that the behavior has changed since I see label changes... but I noticed the highlights were extremely sparse right now. So here is some updated testing:

Zero highlights:
https://mark2cure.org/task/relation/1433/
https://mark2cure.org/task/relation/1451/
https://mark2cure.org/task/relation/1510/
https://mark2cure.org/task/relation/1481/
https://mark2cure.org/task/relation/1435/
https://mark2cure.org/task/relation/1439/
https://mark2cure.org/task/relation/1494/
https://mark2cure.org/task/relation/1460/

Gene only is highlighted:
https://mark2cure.org/task/relation/1521/
https://mark2cure.org/task/relation/1458/

Disease only is highlighted:
https://mark2cure.org/task/relation/1501/

[JTFouquier]

@x0xMaximus, For the highlights it looks like this line in ypet is very often returning empty arrays for "var annotations" which is causing the highlights to be so sparse. When you see highlights, the array contains items. So something is wrong with "passage.annotations" in ypet because the "if(passage)" is always being evaluated. If you test with the links I provided last time, you can see this behavior. I know I'm behind, so sorry if this is old news. :)

[gtsueng]

Apparently the lack of highlighting in the relationship module has gotten so bad that users were offering to contribute highlights for them.

Some missing highlights in the relationship task as reported by users:
PMID 10929009: 2/3 missing highlights- 1st pair asked about GDP-mannose & GDP-Mannose deficiency. Nothing highlighted. 2nd pair asked about N-glycosylation & mannoslyphosphoryldolichol. The only highlighted word was "deficiencies." 3rd pair asked about P-P-dol & congenital disorders of glycosylation. Nothing was highlighted

PMID: 10980531 1.5/2 missing highlights: 1st pair (CDG-1b to protein losing enteropathy) Only CDG-1b was highlighted & that was only in the title ... not in the text. 2nd pair asked about mannose-6-phosphate & protein losing enteropathy. Nothing was highlighted.

PMID: 21384228 2/3 missing highlights: 1st RD asked about dolichol & O-glucosylation and had 3 "dolichol" words highlighted - on lines 3, 5, & 10 (but there were more in the title & abstract). The 1st RD also had "dolichol-P-mannose" highlighted on line 6 ... but that was not a concept to consider. There were no highlights for O-glycosylation. 2nd RD asked for dolichol-P-mannose & glycosylation disorders. Nothing was highlighted. 3rd RD asked for polyprenol & glycosylation disorders. Nothing was highlighted.

PMID 10914684: 1.5/2 missing highlights: 1st pair asked about N-glycan and glucosyltransferase. Nothing was highlighted. 2nd RD asked about oligosaccharides and genetic diseases. Only "genetic diseases" was highlighted.

[gtsueng]

Missing highlights plagues majority of relationships. Of the 25 abstracts for relationship work displayed on my dashboard:

• Highlights not missing: 1
• Task is completed, and cannot be further inspected (no idea why it's even available on dashboard): 1
• Highlights missing for concept 1 AND concept 2: 2
  (note in both cases, the concepts are part of a longer phrase linked by "-"
• Highlights missing for just concept 2: 21

[x0xMaximus]

Extremely correlated to #204 - we now treat highlights the same if they're the users's or opponents so they're even more related now than they were