One event may yield multiple sentences likely due to superscript references after sentence end.

JULIELab / gepi

GePI (GEne - Protein Interactions) is a web portal for quick and convenient access to gene - protein interaction mentions automatically extracted from the biomedical literature, i.e. PubMed and PubMed Central (Open Access Subset).

GNU General Public License v3.0

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One event may yield multiple sentences likely due to superscript references after sentence end. #63

Open SchSascha opened 7 years ago

SchSascha commented 7 years ago

Example gepi input: AList: 196 yields:

PMC id:
- PMC4303521
sentence:
- The activated AHR/ARNT complex binds dioxin-response elements (DREs) in the upstream promoter of AHR-regulated genes and modulates their expression.1 AHR regulates a diverse array of target genes including xenobiotic metabolizing enzymes,1 cell cycle proteins,2 ribosyltransferases,3 and others.1 Ligands for AHR include persistent organic pollutants such as 2,3,7,8-tetracholorodibenzo-p-dioxin (TCDD) and other polyhalogenated and nonhalogenated polycyclic aromatic hydrocarbons, tryptophan UV-photoproducts (FICZ), dietary indole-3-carbanol derivatives (DIM), and molecules endogenous to the liver such as 3-indoxyl sulfate.1,4,5 Potent xenobiotic AHR ligands, such as TCDD (Supporting Fig. S1), produce toxicities in rodents, including hepatotoxicity, immune suppression, epithelial hyperplasia, and tumor promotion in multiple tissues.1 Activation of AHR (Fig.

SchSascha commented 6 years ago

Further example:

PMC4471790
While MK-2206 is equally potent against Akt1 and Akt2, it is far less potent against Akt3.32,33 Another Akt inhibitor Akti1/2, which is an ATP non-competitive inhibitor, also inhibits Akt1 and Akt2.32,34 In contrast, SBF-1, a synthetic steroidal glycoside, blocks the interaction between PDK1 and Akt3, and, thus, could be applied to target melanoma growth and metastasis.35 In conclusion, the present study has revealed the previously undiscovered function of Akt-isoforms and AKT genes as potential regulators of pathobiological behavior in lung carcinomas; that is, the critical involvement of Akt1/AKT1 and Akt2/AKT2 in tumors harboring “FISH-positive” increase of AKT1/AKT2 (22.1%), but not of Akt3/AKT3.

khituras commented 6 years ago

I did change the PMC reader to omit all xref elements. Those elements are responsible to hold references to footnotes, bibliography, tables and what else. Before, we only omitted footnote references. I think I was kind of conservative there. Now we just omit references altogether. However, this required a complete reprocessing of PMC.

SchSascha commented 6 years ago

If I am not mistaken this is not included in the index currently used, right?

khituras commented 6 years ago

Right.

On 1. Dec 2017, at 23:37, SchSascha notifications@github.com wrote:

If I am not mistaken this is not included in the index currently used, right?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/khituras/gepi/issues/63#issuecomment-348632867, or mute the thread https://github.com/notifications/unsubscribe-auth/AEbucOg7MIfM-m17huGyhgw2xJta-wH6ks5s8H-ngaJpZM4PI12t.

SchSascha commented 5 years ago

Still needs to be open?

khituras commented 5 years ago

I would let it open until we see in the current GePi version that this exact issue on that exact document is gone.

SchSascha commented 5 years ago

Good.