PathwayCommons / factoid

A project to capture biological pathway data from academic papers
https://biofactoid.org
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Capture paper relations #1203

Closed jvwong closed 7 months ago

jvwong commented 1 year ago

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 https://github.com/PathwayCommons/factoid/issues/961#issuecomment-1710749298

jvwong commented 1 year ago

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

PubMedArticle: CommentsCorrections

<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 commented 1 year ago

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: https://github.com/PathwayCommons/factoid/issues/961#issuecomment-1645461211

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 commented 1 year ago

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

jvwong commented 1 year ago

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 commented 7 months ago
jvwong commented 7 months ago

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