SoFairOA/SoFairVerifier

Model for validating software mention candidates.

Input

The model expects text with software mention that should be verified. The candidate must be enclosed in tags. If Available it also expects search results obtained for given candidate.

There is en example of input for the model:

GOSeq (52). RPKM calculations in features were done using  <verify> bedtools </verify>  (53). CLIPseq/RNA-seq coverage plots were calculated using cover-ageBed from the bedtools toolset and visualized using custom scripts in


Search results for the target candidate are:

{"title":"bedtools: a powerful toolset for genome arithmetic —","link":"https://bedtools.readthedocs.io/en/latest/","snippet":"As of version 2.18, bedtools is substantially more scalable thanks to improvements we have made in the algorithm used to process datasets that are ..."}

{"title":"The BEDTools suite — bedtools 2.31.0 documentation","link":"https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html","snippet":"bedtools consists of a suite of sub-commands that are invoked as follows: ... The full list of bedtools sub-commands."}

{"title":"intersect — bedtools 2.31.0 documentation","link":"https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html","snippet":"By default, bedtools intersect will report an overlap between A and B so long as there is at least one base pair is overlapping."}

{"title":"Installation — bedtools 2.31.0 documentation","link":"https://bedtools.readthedocs.io/en/latest/content/installation.html","snippet":"Installing bedtools involves either downloading the source code and compiling it manually, or installing stable release from package managers such as ..."}

{"title":"coverage — bedtools 2.31.0 documentation","link":"https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html","snippet":"For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a ..."}

{"title":"GitHub - arq5x/bedtools2: bedtools - the swiss army knife for","link":"https://github.com/arq5x/bedtools2","snippet":"As of version 2.18, bedtools is substantially more scalable thanks to improvements we have made in the algorithm used to process datasets that are ..."}

{"title":"'bedtools' tag wiki - Bioinformatics Stack Exchange","link":"https://bioinformatics.stackexchange.com/tags/bedtools/info","snippet":"For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic ..."}

{"title":"BEDTools: a flexible suite of utilities for comparing genomic","link":"https://pubmed.ncbi.nlm.nih.gov/20110278/","snippet":"BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that ..."}

{"title":"BEDTools: The Swiss-Army Tool for Genome Feature Analysis","link":"https://pubmed.ncbi.nlm.nih.gov/25199790/","snippet":"Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools operations may be combined to create bespoke pipelines ..."}

{"title":"dna sequence - How to use bedtools coverage to assess genome","link":"https://stackoverflow.com/questions/53733419/how-to-use-bedtools-coverage-to-assess-genome-assembly","snippet":"I have been attempting to use \\" bedtools coverage\\" command to try and assess the coverage of my genomic assembly and the existance of any inversions ..."}

There is jinja2 template used for training the model:

{{marked_input_text}}
  
{% if search_results | length > 0 %}
Search results for the target candidate are:
{% for r in search_results %}
{{r | model_dump_json}}
{%endfor %}
{% endif %}