Documentation for exported Literature classifiers #2425
Description
Background/Explanation
Curatable classifiers
Currently, we only have one curatable classifier for gene-specific publications.
This will be relabelled from
Curatable-> "Curatable Gene-specific functional data"
Papers containing sequence datasets still need to be read and datasets hosted ( takes substantial curation effort)
We export these in the "curated _publications.tsv) dataset.
i.e.
curated_publications.tsv | Publications that have been manually curated by PomBase. Some of these publications do not contain gene-specific data (for example browser datasets, or sequence features)
To make this clearer, all of the sequence feature labels will be exported as
Curatable, sequence features and regions
The following existing qualifiers are subtypes of "Curatable, sequence features and regions"
with only a small numbers of assigned publications. These labels are used mainly for workflow management and will and will be mapped up to "Curatable, sequence features and regions"
• Sequence feature or region
◦ Browser datasets, to host
◦ Browser datasets, hosted
◦ DNA replication related
◦ DNA recombination
◦ Mitochondrial sequence related
◦ 3D genome organization
◦ Transposon related
◦ Mating-type related
Result
| Category | Description |
|---|---|
| Curatable Gene-specific functional data | Publications containing gene-specific functional data related to S. pombe |
| Curatable, sequence features and regions | Publications containing sequence-specific data related to S. pombe (i.e sequence feature coordinates, genome browser tracks |
The remainder are "uncuratable" publication classifiers, described here:
Uncuratable classifiers
| Category | Description |
|---|---|
| Publication inaccessible | We are unable to access the publication by any mechanism |
| Mutagenicity or toxicity study | Studies of the effects of drugs or other chemical compounds on S. pombe in a wild-type background — no gene-specific information |
| Not physically mapped | The physical identity of the protein described is unknown |
| Biotech | Characterization of yeasts in fermentations, use in fermentation, recombinant protein/metabolite production, etc. |
| Modelling | Theoretical modelling is out of scope for PomBase |
| Duplicated in PubMed | Some publications have been indexed twice by PubMed in error |
| Database | Publications describing databases, tools, and resources relevant to S. pombe but containing no gene-specific experimental data |
| Bioarchive | Papers from pre-print servers. PomBase does not currently curate pre–peer review manuscripts |
| Wrong organism | The publication mentions fission yeast or S. pombe in the title, abstract, or keywords, but contains no S. pombe experiments |
| Phylogeny and evolutionary studies | Studies related to the evolutionary classification of species or protein families |
| Cell composition or WT feature | Features describing a general characteristic of the species that cannot be assigned to a specific gene or genes (e.g., cell size, morphology) |
| Method or reagent | Publication describes a method or reagent that can be used in fission yeast experiments but does not include any gene-specific data |
| Review or Comment | A review or commentary related to some aspect of fission yeast biology, but excluding experimental data |
| Erratum | An erratum notice lists corrections to typos, factual mistakes, or formatting errors discovered after publication. An erratum will not usually affect the original interpretation |
| Not English | In scope but not published in English; currently such manuscripts are not routinely curated by PomBase |
| Bioinformatics | Bioinformatics analysis with no gene-specific experimental data |
| Loaded in error | Papers which are not related to fission yeast, loaded by the PubMed pipeline or selected manually by users to test Canto |
| Other | Uncuratable papers that cannot be classified as any other listed types |
| Retracted | Publication that has been formally withdrawn from the scientific or scholarly record because it is found to be unreliable or seriously flawed after publication |
@afg1 This documantation will be included with AI datasets shortly
@PCarme
Let us know if there are any questions