Hi Ben. On reflection, I think the SPATA5 page is more about the gene, than the protein, despite the lead (and only) sentence which has the protein as its subject. The other example from the RFC (Neurophysin I) seems less clearcut to me since the text is entirely about the protein, while the infobox is the only thing talking about the gene. I generally discount infoboxes since they can have little to do with the main subject of the page (e.g. civil war battle with infoboxes about the opposing generals or the associated NRHP place). 

Despite the textual confusion, I realized that there isn't really much merge risk here since the "encodes" property linking the gene and the protein should prevent any attempted merge from happening.

Tom

On Tue, Jun 14, 2016 at 3:20 PM, Benjamin Good <ben.mcgee.good@gmail.com> wrote:
Hi Tom,

I think the example you have there is actually linked up properly at the moment?
https://en.wikipedia.org/wiki/SPATA5 is about both the gene and the protein as are most Wikipedia articles of this nature.  And it is linked to the gene the way we encourage modeling https://www.wikidata.org/wiki/Q18052679  - and indeed the protein item is not linked to a Wikipedia article again following our preferred pattern.

For the moment...  _our_ merge problem seems to be mostly resolved.  Correcting the sitelinks on the non-english Wikipedias in a big batch seemed to help slow the flow dramatically.  We have also introduced some flexibility into the Lua code that produces infobox_gene on Wikipedia.  It can handle most of the possible situations (e.g. wikipedia linked to protein, wikipedia linked to gene) automatically so that helps prevent visible disasters..  

On the main issue you raise about merges..  I'm a little on the fence.  Generally I'm opposed to putting constraints in place that slow people down - e.g. we have a lot of manual merge work that needs to be done in the medical arena and I do appreciate that the current process is pretty fast.  I guess I would advocate a focus on making the interface more vehemently educational as a first step.  E.g. lots of 'are you sure' etc. forms to click through but ultimately still letting people get their work done without enforcing an approval process.   

-Ben

On Tue, Jun 14, 2016 at 10:53 AM, Tom Morris <tfmorris@gmail.com> wrote:
Bad merges have been mentioned a couple of times recently and I think one of the contexts with Ben's gene/protein work.

I think there are two general issues here which could be improved:

1. Merging is too easy. Because splitting/unmerging is much harder than merging, particularly after additional edits, the process should be biased to mark merging more difficult.

2. The impedance mismatch between Wikidata and Wikipedias tempts wikipedians who are new to wikidata to do the wrong thing.

The second is a community education issue which will hopefully improve over time, but the first could be improved, in my opinion, by requiring more than one person to approve a merge. The Freebase scheme was that duplicate topics could be flagged for merge by anyone, but instead of merging, they'd be placed in a queue for voting. Unanimous votes would cause merges to be automatically processed. Conflicting votes would get bumped to a second level queue for manual handling. This wasn't foolproof, but caught a lot of the naive "these two things have the same name, so they must be the same thing" merge proposals by newbies. There are lots of variations that could be implemented, but the general idea is to get more than one pair of eyes involved.

A specific instance of the structural impedance mismatch is enwiki's handling of genes & proteins. Sometimes they have a page for each, but often they have a single page that deals with both or, worse, a page who's text says its about the protein, but where the page includes a gene infobox.

This unanswered RFC from Oct 2015 asks whether protein & gene should be merged: https://www.wikidata.org/wiki/Wikidata:Requests_for_comment/Oxytocin_and_OXT_gene

I recently ran across a similar situation where this Wikidata gene SPATA5 https://www.wikidata.org/wiki/Q18052679 is linked to an enwiki page about the associated protein https://en.wikipedia.org/wiki/SPATA5, while the Wikidata protein is not linked to any wikis https://www.wikidata.org/wiki/Q21207860

These differences in handling make the reconciliation process very difficult and the resulting errors encourage erroneous merges. The gene/protein case probably needs multiple fixes, but many mergers harder would help.

Tom



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