Wikidata:Property proposal/pathway annotation

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pathway annotation[edit]

Originally proposed at Wikidata:Property proposal/Natural science

   Withdrawn

Motivation[edit]

Working on annotating biological pathway items. Linking these to annotations, like disease and pathway ontology terms, will enhance their value in Wikidata. --AlexanderPico (talk) 00:03, 9 October 2019 (UTC)

Discussion[edit]

PubMed (near bottom of page) and Identifiers.org use the term "keywords" for basically this purpose.

"keywords" are indeed commonly used in scientific publishing. They are very generic, however, and not synonymous or as clearly defined as "pathway annotation". The "main subject" property includes "keywords" as one of over a dozen aliases. This property is arguably even more vague than "keywords". So, the proposal stands for a new property with more clearly defined use. --AlexanderPico (talk) 17:32, 10 October 2019 (UTC)

Context for background/future work and reasons why they are not appropriate for this proposed use:

Andrew Su
Marc Robinson-Rechavi
Pierre Lindenbaum
Michael Kuhn
Boghog
Emw
Chandres
Dan Bolser
Pradyumna
Chinmay
Timo Willemsen
Salvatore Loguercio
Tobias1984
Daniel Mietchen
Optimale
Mcnabber091
Ben Moore
Alex Bateman
Klortho
Hypothalamus
Vojtěch Dostál
Gtsulab
Andra Waagmeester
Sebotic
Mvolz
Toniher
Elvira Mitraka
David Bikard
Dan Lawson
Francesco Sirocco
Konrad U. Förstner (talk)
Chris Mungall (talk)
Kristina Hettne
Hardwigg
i9606
Putmantime
Tinm
Karima Rafes
Finn Årup Nielsen
Jasper Koehorst
Till Sauerwein
Crowegian
Nothingserious
Okkn
AlexanderPico
Amos Bairoch
Gstupp
DePiep
Was a bee
SarahKeating
Muhammad Elhossary
Ptolusque
Netha
Damian Szklarczyk
Kpjas
Thibdx
Juliansteinb
TiagoLubiana
SCIdude
Pictogram voting comment.svg Notified participants of WikiProject Molecular biology

  • Symbol oppose vote.svg Oppose See discussion below. AlexanderPico (talk) 00:15, 9 October 2019 (UTC)
  • Symbol support vote.svg Support Andrew Su (talk) 04:43, 9 October 2019 (UTC)
  • Symbol support vote.svg Support Andrawaag (talk) 17:28, 9 October 2019 (UTC)
  • Symbol support vote.svg Support. YULdigitalpreservation (talk) 17:30, 9 October 2019 (UTC)
  • Symbol wait.svg Wait Ariutta (talk) 00:45, 10 October 2019 (UTC)
  • Symbol support vote.svg Support David (talk) 14:21, 10 October 2019 (UTC)
  • Symbol oppose vote.svg Oppose Excellent point, but it is a very broad property, meaning "some kind of relation". For the examples in the proposal, a modification of main subject to accomodate biological pathways would be enough. A biological pathway is a set of inter-connected reactions and interactions whose delineation and scope are used as a model". The set assembled by the community can be seen as a piece of work, subjected to curation and changes, which has "main subjects". TiagoLubiana (talk) 20:37, 10 October 2019 (UTC)
Right. "main subject" is certainly broad enough to encompass our intended use here (like the examples in the proposal). But since we have a very specific use in mind, we thought it would be better to mint a more specific property. It's not just the specificity of subjects (bioloigcal pathways), but also the specificity of objects (ontology-backed annotations), like diseases, cell types and processes. If I could capture more of this specificity in the proposal, would you be persuaded? Or is your argument that since an existing property *could* work (frankly, because it is so vague) we should just use it? --AlexanderPico (talk) 00:12, 11 October 2019 (UTC)
The ontologies include disease, cell type and pathway type. Option #1 is to use pathway_annotation for all, e.g.: pathway → pathway_annotation → cancer + pancreatic_ductal_cell + cancer_pathway. Option #2 would just replace pathway_annotation with main_subject. Option #3 is to use a different property for each ontology, e.g., something like pathway → medical_condition → cancer; pathway → anatomical_location → pancreatic_ductal_cell; pathway → main_subject → cancer_pathway. --Ariutta (talk) 23:56, 11 October 2019 (UTC)
Ooh, option #3 sounds like a "baby bear" solution: not too vague, not too specific, but rather just right! Should I retract this proposal? How do I formally do that? --AlexanderPico (talk) 02:21, 12 October 2019 (UTC)
If you want to withdraw it you can edit the for above to say "status = withdrawn". ChristianKl❫ 16:27, 14 October 2019 (UTC)
Agreed. See discussion right above this one. How do I formally close or withdraw this proposal? I'll try removing it from the list. --AlexanderPico (talk) 17:15, 14 October 2019 (UTC)
Overview of leukocyte-intrinsic Hippo pathway functions (Q66104607) is about a pathway model. It cites a paper that was used as a reference to construct the model. The paper is part of the pathway's bibliography . --AlexanderPico (talk) 17:15, 14 October 2019 (UTC)
@AlexanderPico: A pathway doesn't cite a paper or has authors. It also shouldn't be named 'Overview of'. An item about the paper could link to the pathway item with main subject (P921). ChristianKl❫ 12:41, 23 October 2019 (UTC)