DOI: 10.5281/zenodo.2562938
title: Hackathon - TF-TG literature triage Gold Standard corpus

description: This link contains the gold standard corpus for training the systems aiming at classifying or triaging the documents (PubMed abstracts) in relevant or not relevant for TF-TG relations. Note that this is not purely a curation triage, but we are primarily looking whether the abstracts do describe/characterize TF-TG interactions (positive training set labeled as “1” or they don't (negative training set labeled as “0”).  

This dataset was manually classified by domain experts into these to classes.

Note that in PubMed there is a very considerable class imbalance, implying that there is only a very small fraction of TF-TG relations relevant literature subset. The resulting classifier should be useful to triage the entire PubMed database.


	
	Name: greekc_triage_training_v02.tsv
	
	
	Example:
	


11731616    [{"sourceid":"11731616","sourcedb":"PubMed","text":"Homeobox protein Gsh-1-dependent regulation of the rat GHRH gene promoter. Although GHRH is known to play a pivotal role in the regulation of the GHRH-GH-IGF-I axis, the molecular mechanism of GHRH gene expression has not yet been examined. Here we studied the transcriptional regulation of the GHRH gene 5'promoter using an in vitro experimental model system. We especially focused on the role of homeobox transcriptional factor Gsh-1, because a dwarf phenotype and abolished GHRH expression was observed in Gsh-1 knockout mice. First, we cloned human Gsh-1, which showed 87.3% homology with mouse Gsh-1 at the nucleotide level. When the 5'-promoter region of the rat GHRH gene was introduced into the human placental cell line JEG-3, in which we found the endogenous expression of Gsh-1 as well as GHRH mRNA, substantial transcriptional activity of the promoter was recognized. Promoter activity was further enhanced by overexpression of Gsh-1 protein, whereas it was substantially reduced by elimination of Gsh-1 binding sites. EMSA confirmed the actual binding of Gsh-1 on the multiple binding sites of GHRH gene promoter. Finally, coexpression of CREB-binding protein significantly enhanced the Gsh-1-induced GHRH gene expression, suggesting the cooperative role of the coactivator protein. Because Gsh-1 is found to be expressed in the hypothalamus of the adult rat, our data provide evidence that the Gsh-1 homeobox protein plays a key role in the expression of the GHRH gene.","denotations":[{"obj":"Gene:29446","span":{"begin":84,"end":88}},{"obj":"Gene:288457","span":{"begin":17,"end":22}},{"obj":"Gene:29446","span":{"begin":55,"end":59}},{"obj":"Gene:29446","span":{"begin":146,"end":150}},{"obj":"Gene:29446","span":{"begin":193,"end":197}},{"obj":"Gene:29446","span":{"begin":295,"end":299}},{"obj":"Gene:14842","span":{"begin":430,"end":435}},{"obj":"Gene:14601","span":{"begin":477,"end":481}},{"obj":"Gene:14842","span":{"begin":509,"end":514}},{"obj":"Gene:219409","span":{"begin":553,"end":558}},{"obj":"Gene:14842","span":{"begin":599,"end":604}},{"obj":"Gene:29446","span":{"begin":669,"end":673}},{"obj":"Gene:219409","span":{"begin":783,"end":788}},{"obj":"Gene:2691","span":{"begin":800,"end":804}},{"obj":"Gene:288457","span":{"begin":940,"end":945}},{"obj":"Gene:288457","span":{"begin":1010,"end":1015}},{"obj":"Gene:288457","span":{"begin":1068,"end":1073}},{"obj":"Gene:29446","span":{"begin":1107,"end":1111}},{"obj":"Gene:54244","span":{"begin":1152,"end":1172}},{"obj":"Gene:288457","span":{"begin":1200,"end":1205}},{"obj":"Gene:29446","span":{"begin":1214,"end":1218}},{"obj":"Gene:288457","span":{"begin":1304,"end":1309}},{"obj":"Gene:288457","span":{"begin":1408,"end":1413}},{"obj":"Gene:29446","span":{"begin":1473,"end":1477}}]}]    1


	
	Format: tsv-separated columns (PMID, PubAnnotation JSON formated results of Pubtator for this record together with the automatically detected gene mentions using GnormPlus providing the Entrez Gene Identifiers together with the mention offsets, i.e. start and end character positions, corresponding class label of the records (1= relevant, 0=nonrelevant))
	
	
	PubAnnotation format description: http://www.pubannotation.org/docs/annotation-format/
	
	
	PubTator record retrieval description:
	


https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/curl.html

<strong>Remember:</strong> One must notice that this dataset is high imbalanced, with very few cases of the positive class. The additional files could also be explored to build the model or even to build a classifier working at the level of sentences instead of abstracts,