Difference between revisions of "Textpresso"

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==Pipeline Description==
 
==Pipeline Description==

Revision as of 04:29, 6 June 2009

Textpresso for WormBase Curation

This page will serve as a platform to coordinate the automated curation efforts of Textpresso for WormBase. First two items cover general tool and website feature requests. Then, curation pipelines for each datatype are listed. Each section has subsections description, requests, false positives and false negatives.

The description section includes a detailed description of the Textpresso pipeline for that data type. Details would include the type of search performed, the papers included or excluded, how often the search is run, etc. The requests postings request addition or changes to procedures in the pipeline for that particular data type. In the false positive cases section people could post false positive search results with a brief description of why they think it happened. The false negative cases is the same as for false positives.

Contents

Curation Tools and Tool Feature Requests

Textpresso Website Feature Requests

C. elegans antibody

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Integrated transgenes

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Small scale RNAi

Pipeline Description

Requests

False Positive Cases

False Negative Cases

GO cellular component

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Newly created allele

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Email addresses

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Content of corpus

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Alleles, transgenes, rearrangements

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Gene-gene interaction

Pipeline Description

Requests

False Positive Cases

False Negative Cases


Functional complementation

  • Pipeline Description: Not actively curated
  • Requests
  • False Positive Cases
  • False Negative Cases



Gene product interaction

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Protein analysis in vitro

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Domain analysis

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Covalent modification

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Mass spectrometry

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Transgenes used as tissue marker

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Gene structure correction

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Sequence mutant alleles

Pipeline Description

Requests

False Positive Cases

False Negative Cases

New SNPs

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Species (C. elegans, C. elegans other than Bristol, Nematode other than C. elegans, non-nematode species)

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Genes studied in this paper

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Gene mapping data

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Overexpression phenotypes

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Tissue or cell site of action

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Molecular function of a gene product

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Relevance to a human disease

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Phenotype analysis

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Mosaic analysis

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Time of (gene) action

Pipeline Description

Requests

False Positive Cases

False Negative Cases

New expression pattern for a gene

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Alteration in gene expression by genetic or other treatment

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Regulatory sequence features

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Position frequency matrix (PFM) or position weight matrix

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Structural information

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Cell function

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Phylogenetic data

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Microarray

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Other bioinformatics analysis

Pipeline Description

Requests

False Positive Cases

False Negative Cases

Supplemental Material

Pipeline Description

Requests

False Positive Cases

False Negative Cases

None of the aforementioned data types are in this research article

Requests

--MMuller 16:14, 5 June 2009 (EDT)