Capture paper relations

[jvwong]

It's worth considering adding in an extra field for PubMed and CrossRef data to capture relations between preprints and articles.

Source	ID Type	Article type attribute	Publishers Supported	Relations
PubMed	PubMed uid (optional [PMCID, DOI])	<PublicationType> (MESH: D000076942)	bioRxiv; medRxiv; arXiv; Research Square	child, parent
CrossRef	Digital Object Identifier	type: posted-content; subtype: preprint	multiple (members)	child, parent, equivalent

Originally posted by @jvwong in #961 (comment)

[jvwong]

Sample for "The ATM-E6AP-MASTL axis mediates DNA damage checkpoint recovery." eLife 3023. PMID: 37672026; DOI: 10.7554/eLife.86976

PubMedArticle: CommentsCorrections

• https://pubmed.ncbi.nlm.nih.gov/help/#comment-correction
• Medline Element: Comments/Corrections

<CommentsCorrectionsList>
  <CommentsCorrections RefType="UpdateOf">
	  <RefSource>doi: 10.1101/2023.02.22.529521</RefSource>
  </CommentsCorrections>
  <CommentsCorrections RefType="UpdateOf">
	  <RefSource>doi: 10.7554/eLife.86976.1</RefSource>
  </CommentsCorrections>
  <CommentsCorrections RefType="UpdateOf">
	  <RefSource>doi: 10.7554/eLife.86976.2</RefSource>
  </CommentsCorrections>
</CommentsCorrectionsList>

CrossRef Work relations

"relation": {
	"has-preprint": [
		{
			"id-type": "doi",
			"id": "10.7554\/eLife.86976.2",
			"asserted-by": "subject"
		}
	],
	"is-same-as": [
		{
			"id-type": "doi",
			"id": "10.7554\/eLife.86976.3",
			"asserted-by": "subject"
		}
	],
	"is-version-of": [
		{
			"id-type": "doi",
			"id": "10.7554\/eLife.86976.1",
			"asserted-by": "subject"
		},
		{
			"id-type": "doi",
			"id": "10.7554\/eLife.86976.2",
			"asserted-by": "subject"
		}
	]
},

[jvwong]

All of the noted articles unrecognized by Biofactoid on initial submission (i.e. they were preprints) got updated by the CRON to their respective eLife Version of Record: #961 (comment)

We should keep this in mind regarding any update strategy. For instance, if we support a preprint and only update that (not a subsequent publication with the same title) it would be nice to link that to the publication in Biofactoid, make that obvious, so the author doesn't feel they need to create another record.

[maxkfranz]

Are you thinking of having two links, one for the preprint and one for the published article?

[jvwong]

Yes. A primary one (for the current paper) and a secondary one (e.g. relation is: has version, has preprint, or has publication).

I think bioRxiv and PubMed both do this now.

[jvwong]

• Sub-Tasks
  • relations: PubMed article CommentsCorrectionsList (Capture PubMed article CommentsCorrectionsList  #1247)
  • relations: Crossref work relation information
  • update: Check for PubMed updates for any Document with publication type preprint
    • Case 1: Document for preprint updates with relation UpdateIn pointing to VOR
    • Case 2: Document has no relation - search PubMed.
  • UI: to reflect relations

[jvwong]

eLife Reviewed Preprints that eventually moved on to a Version of Record (VOR)

created	doi	id	journal	pmid	title	type	VOR
2023-11-30	10.7554/elife.87510.3	a5f9c7ef-4ba0-46a4-b410-5157bc3d12e7	elife		A positive feedback loop between ZEB2 and ACSL4 regulates lipid metabolism to promote breast cancer metastasis	Preprint	Y
2023-12-13	10.7554/elife.88637.2	d3a5b322-661d-4b9f-8996-8cf881dbe9da	elife		Ulk4 promotes Shh signaling by regulating Stk36 ciliary localization and Gli2 phosphorylation	Preprint	Y
2023-12-26	10.7554/elife.89835.2	b3c87835-7976-4e50-9949-23e1039416e2	elife		Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and to promote Dbp5 mediated tRNA export in vivo	Preprint	Y
2023-12-28	10.7554/elife.88328.3	667182df-ff59-4cec-abf4-96e2a3873e38	elife		Comparative Interactome Analysis of α-arrestin Families in Human and Drosophila	Preprint	Y
2024-01-09	10.7554/elife.90184.3	1b257dab-095b-4a63-8e57-60edbf32ff9a	eLife Sciences Publications, Ltd		14-3-3 protein augments the protein stability of phosphorylated spastin and promotes the recovery of spinal cord injury through its agonist intervention	Preprint	Y
2024-01-10	10.7554/elife.88808.3	f0eb960f-15b3-40d0-a16c-6eeae35ffe06	eLife Sciences Publications, Ltd		Orai mediated Calcium entry determines activity of central dopaminergic neurons by regulation of gene expression	Preprint	Y
2024-01-23	10.7554/elife.90192.2	94f6073c-5567-4f40-bdce-a84719873463	eLife Sciences Publications, Ltd		Heparan sulfate promotes TRAIL-induced tumor cell apoptosis	Preprint	Y
2024-01-24	10.7554/elife.87559.3	01d5460e-c42c-4110-8f2b-b184b4dbc7ba	eLife Sciences Publications, Ltd		Coupling of Slack and NaV1.6 sensitizes Slack to quinidine blockade and guides anti-seizure strategy development	Preprint	Y
2024-02-02	10.7554/elife.92731.2	d2827061-7442-4a1d-a81c-71bc2ae1fd29	eLife Sciences Publications, Ltd		Depletion of SMN Protein in Mesenchymal Progenitors Impairs the Development of Bone and Neuromuscular Junction in Spinal Muscular Atrophy	Preprint	Y
2024-02-12	10.7554/elife.87386.2	a6068a85-beff-422c-b221-4d854528b0cf	elife		The acetylase activity of Cdu1 regulates bacterial exit from infected cells by protecting Chlamydia effectors from degradation	Preprint	Y
2024-02-20	10.7554/elife.88565.2	9f960e8a-8340-46cb-9955-c1b27fe0d271	elife		Delta-dependent Notch activation closes the early neuroblast temporal program to promote lineage progression and neurogenesis termination in Drosophila	Preprint	Y
2024-02-28	10.7554/elife.90051.3	adcf7c9e-74f2-406e-a511-90a5a8d28d34	eLife Sciences Publications, Ltd		Neuronal NPR-15 modulates molecular and behavioral immune responses via the amphid sensory neuron-intestinal axis in C. elegans	Preprint	Y
2024-03-04	10.7554/elife.93013.2	dd2da1ca-fc9f-4cf3-bba2-6e9937179945	eLife Sciences Publications, Ltd		The non–muscle actinopathy–associated mutation E334Q in cytoskeletal γ– actin perturbs interaction of actin filaments with myosin and ADF/cofilin family proteins	Preprint	Y
2024-03-06	10.7554/elife.91218.2	a032f12a-fe30-44e7-b4b5-b8f27b89cf0a	eLife Sciences Publications, Ltd		A binding site for phosphoinositides described by multiscale simulations explains their modulation of voltage gated sodium channels	Preprint	Y
2024-03-06	10.7554/elife.89045.3	8f846123-d500-4740-a016-92e5ddf6634d	eLife Sciences Publications, Ltd		Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis	Preprint	Y
2024-03-09	10.7554/elife.88772.3	405c7f93-f10b-4b28-ab8d-be532dec745a	eLife Sciences Publications, Ltd		Imidacloprid disrupts larval molting regulation and nutrient energy metabolism, causing developmental delay in honey bee Apis mellifera	Preprint	Y
2024-03-14	10.7554/elife.92755.2	60188d5a-8dc8-4d94-8f01-e6d7cddf850f	eLife Sciences Publications, Ltd		Rho GTPase signaling and mDia facilitate endocytosis via presynaptic actin	Preprint	Y
2024-03-16	10.7554/elife.91040.2	7df07c27-0f7a-4223-b685-be33231e405a	eLife Sciences Publications, Ltd		Purine nucleosides replace cAMP in allosteric regulation of PKA in trypanosomatid pathogens	Preprint	Y
2024-03-17	10.7554/elife.91060.2	9ffc09f3-83a2-4528-9a2b-babf47119327	eLife Sciences Publications, Ltd		Intermittent fasting promotes ILC3s secreting IL-22 contributing to the beigeing of white adipose tissue	Preprint	N
2024-03-23	10.7554/elife.89938.3	bb3983f5-8d1b-4e20-86ea-c63e14c460ee	eLife Sciences Publications, Ltd		Membrane contact sites regulate vacuolar fission via sphingolipid metabolism	Preprint	Y
2024-03-25	10.7554/elife.89613.2	cdfe5b24-967c-4a7e-b255-13ed940ac87d	eLife Sciences Publications, Ltd		Mechanically stimulated osteocytes maintain tumor dormancy in bone metastasis of non-small cell lung cancer by releasing small extracellular vesicles	Preprint	Y
2024-03-29	10.7554/elife.90820.2	fa58260a-701a-4f16-a610-dc22c1ee6bb0	eLife Sciences Publications, Ltd		Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization	Preprint	Y
2024-04-09	10.7554/elife.90203.2	d2da1116-a42e-4ef2-b89a-c2efe3b79391	eLife Sciences Publications, Ltd		The Rapidly Evolving X-linked miR-506 Family Finetunes Spermatogenesis to Enhance Sperm Competition	Preprint	N
2024-04-12	10.7554/elife.91864.2	3114fc5a-3686-48ba-aacf-41ac678e0026	eLife Sciences Publications, Ltd		Inhibition of the serine protease HtrA1 by SerpinE2 suggests an extracellular proteolytic pathway in the control of neural crest migration	Preprint	N