Data type classes definitions - TextpressoDevelopers/textpresso_classifiers GitHub Wiki

Definition of "positive" class - which characteristics must a paper have to be classified as positive?

Antibody

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Catalyticact

A paper must report experimental results describing catalytic (i.e. enzymatic) activity for a gene product.

Expressioncluster

Geneint

(Guess or criteria going forward) Paper must refer to genetic interactions, that is, a double genetic perturbation phenotype should be compared to single genetic perturbation phenotypes and a control phenotype. Terminology often used to describe genetic interactions includes: "suppression", "suppressed", "suppressing", "enhanced", "enhancement", "enhancing", "epistasis", "epistatic", "genetic interaction", "genetically interact", "interact genetically"

Geneprod

(Guess or criteria going forward) Paper should refer to physical interactions of gene products, for example protein-protein interactions or protein-RNA interactions

Genereg

A paper must include data that demonstrates a relationship (or lack of relationship) between some sort of experimental treatment (eg. mutation in a gene or regulatory sequence, chemical treatment, environmental perturbation, etc.) and the expression levels of a gene/protein or localization of a protein. Expression is often measured via RT-qPCR, reporter genes, northern and western blotting, etc. Large scale assays such as microarray or RNAseq data are identified via a separate pipeline through GEO and curated by Wen, so I would consider papers that only include these experiments as "curation negative", but if the results are validated by RT-qPCR, etc., then I would curate the paper.

Newmutant

(Guess or criteria going forward) Papers should reference mutant phenotypes resulting from genetic variations (e.g. alleles)

Otherexpr

A paper must report result from experiments that have been performed to locate a specific gene product within the anatomy (or life stage) of the nematode via conventional expression pattern analysis -i.e. reporter gene analysis, antibody staining, in situ hybridization (ISH), single molecule FISH, RT-PCR, qPCR, Northern and Western blotting.

Examples of sentences flagged as SVM positive and curation negative (the rationale is that the sentence contains the same language that would be used to describe a bona fide new experiment) WBPaper00052994 . VD neurons were visualized with a Punc-25::gfp transgene, juIs76 [37], which is expressed in GABAergic neurons including the six DDs and 13 VDs, 18 of which extend commissures on the right side of the animal. . ehbp-1 is expressed in all somatic cells including neurons [33]. Furthermore, cell-specific transcriptome profiling indicated that fmo-1, fmo-4 and fmo-5 were expressed in embryonic and adult neurons, including motor neurons.
Examples of SVM positive, curation positive for which authors start from a previously described pattern and add just one sentence with additional findings: . fmo-4::gf pwas expressed strongly in hypodermal cells, excluding the seam cells and vulval cells, consistent with previous studies. We also observed fmo-4::gfpexpression in cells in the ventral nerve cord. . Pfmo-5::fmo-5::gfp was expressed strongly in the intestine as previously reported. We also observed expression along the ventral nerve cord.

Overexpr

(Guess or criteria going forward) Papers should reference overexpression phenotypes resulting from overexpression of a gene product

Rnai

A paper must report results from an experiment that uses RNA interference to knockdown/alter gene expression.