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PathwayCommons / factoid

A project to capture biological pathway data from academic papers
https://biofactoid.org
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Handling mentions of the same interaction between a pair of nodes #367

Closed jvwong closed 5 years ago

jvwong commented 6 years ago

Background: In a longer text (e.g. full-text article), there are often several variations of the same interaction mentioned. This is likely to be the norm rather than the exception.

Issue: In the network, was not clear initially that there were multiple edges between a pair of nodes. Moreover, I could not view/delete them individually. My workaround was to delete everything or go the form and access them individually.

This is related to another issue: Does the Factoid model store original REACH text/offset for the interaction? If so, then it is meaningful which interactions I delete or leave.

Example: See Google Drive /Factoid/Testing/Full_text_articles/wong_mcell_v41_2011_MAIN.txt and resulting document. In this case there are 10 instances of a MYC and E2F1 interaction.

image

gbader commented 6 years ago

Ideally the form would nicely organize these. I.e. group or collapse similar and identical statements and show the original sentences for each.

On Mon, Sep 24, 2018, 9:51 AM Jeffrey, notifications@github.com wrote:

Background: In a longer text (e.g. full-text article), there are often several variations of the same interaction mentioned. This is likely to be the norm rather than the exception.

Issue: In the network, was not clear initially that there were multiple edges between a pair of nodes. Moreover, I could not view/delete them individually. My workaround was to delete everything or go the form and access them individually.

This is related to another issue: Does the Factoid model store original REACH text/offset for the interaction? If so, then it is meaningful which interactions I delete or leave.

Example: See Google Drive /Factoid/Testing/Full_text_articles/wong_mcell_v41_2011_MAIN.txt and resulting document http://unstable.factoid.baderlab.org/document/54052800-3d73-43bc-9f2e-b1cd88935c46/73aca69c-9f12-45af-8fb5-ea9ef0b12c98. In this case there are 10 instances of a MYC and E2F1 interaction.

[image: image] https://user-images.githubusercontent.com/4706307/45955531-2dfcfe80-bfde-11e8-94a7-8eb24a937a11.png

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sacdallago commented 6 years ago

From my understanding: apply filtering on reach output to avoid duplicates. If one interaction is more specific, take that over the generic interaction type. If multiple but different specific interactions, pick whichever.

jvwong commented 5 years ago

I have a PR (#450) for a post-REACH interaction filter. Tested by running full-text from a sample of Molecular Cell 'case studies' through Factoid either without filter (figures, left) or with filter (middle). Also included the hand-crafted document (right).

Clarke et al. PRMT5-Dependent Methylation of the TIP60 Coactivator RUVBL1 Is a Key Regulator of Homologous Recombination. Mol. Cell. Volume 65, Issue 5, 2 March 2017, Pages 900-916

clarke_topInteractions

He et al. mTORC1 Promotes Metabolic Reprogramming by the Suppression of GSK3-Dependent Foxk1 Phosphorylation. Mol. Cell. Volume 70, Issue 5, 7 June 2018, Pages 949-960

he_topInteractions

Jeong et al. A Constitutive Intrinsic Inflammatory Signaling Circuit Composed of miR-196b, Meis2, PPP3CC, and p65 Drives Prostate Cancer Castration Resistance. Mol. Cell. VOLUME 65, ISSUE 1, P154-167, JANUARY 05, 2017

jeong_topInteractions

Jin et al. The PLAG1-GDH1 Axis Promotes Anoikis Resistance and Tumor Metastasis through CamKK2-AMPK Signaling in LKB1-Deficient Lung Cancer. Mol. Cell. Volume 69, Issue 1, 4 January 2018, Pages 87-99.e7

jin_topInteractions

Qian et al. Phosphoglycerate Kinase 1 Phosphorylates Beclin1 to Induce Autophagy. Mol. Cell. VOLUME 65, ISSUE 5, P917-931.E6, MARCH 02, 2017

qian_topInteractions

Willemsen et al. Phosphorylation-Dependent Feedback Inhibition of RIG-I by DAPK1 Identified by Kinome-wide siRNA Screening. Mol. Cell. Volume 65, Issue 3, pp403-415. 8 February 02, 2017

willemsen_topInteractions

Yang et al. Reciprocal Regulation of HIF-1α and LincRNA-p21 Modulates the Warburg Effect. Mol. Cell. Volume 53, Issue 1, 9 January 2014, Pages 88-100

yang_topInteractions

Sang et al. LncRNA CamK-A Regulates Ca2+-Signaling-Mediated Tumor Microenvironment Remodeling. Mol. Cell. Volume 72, Issue 1, 4 October 2018, Pages 71-83.e7

sang_topInteractions