Difference between revisions of "Textpresso"
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| − | + | '''[[Textpresso for WormBase Curation]]''' | |
| + | |||
This page will serve as a platform to coordinate the automated curation efforts of Textpresso for WormBase. | 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. | ||
| + | |||
| + | =Curation Tools and Tool Feature Requests= | ||
| + | |||
| + | =Textpresso Website Feature Requests= | ||
| − | == | + | =C. elegans antibody= |
| + | ==Pipeline Description== | ||
| − | + | ==Requests== | |
| − | |||
| − | |||
| − | |||
| − | |||
==False Positive Cases== | ==False Positive Cases== | ||
| − | |||
| − | |||
==False Negative 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== | ||
| + | |||
| + | ==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== | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | --[[User:MMuller|MMuller]] 16:14, 5 June 2009 (EDT) | ||
Revision as of 20:14, 5 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
- 1 Curation Tools and Tool Feature Requests
- 2 Textpresso Website Feature Requests
- 3 C. elegans antibody
- 4 Integrated transgenes
- 5 Small scale RNAi
- 6 GO cellular component
- 7 Newly created allele
- 8 Email addresses
- 9 Content of corpus
- 10 Alleles, transgenes, rearrangements
- 11 Gene-gene interaction
- 12 Functional complementation
- 13 Gene product interaction
- 14 Protein analysis in vitro
- 15 Domain analysis
- 16 Covalent modification
- 17 Mass spectrometry
- 18 Transgenes used as tissue marker
- 19 Gene structure correction
- 20 Sequence mutant alleles
- 21 New SNPs
- 22 Species (C. elegans, C. elegans other than Bristol, Nematode other than C. elegans, non-nematode species)
- 23 Genes studied in this paper
- 24 Gene mapping data
- 25 Overexpression phenotypes
- 26 Tissue or cell site of action
- 27 Molecular function of a gene product
- 28 Relevance to a human disease
- 29 Phenotype analysis
- 30 Mosaic analysis
- 31 Time of (gene) action
- 32 New expression pattern for a gene
- 33 Alteration in gene expression by genetic or other treatment
- 34 Regulatory sequence features
- 35 Position frequency matrix (PFM) or position weight matrix
- 36 Structural information
- 37 Cell function
- 38 Phylogenetic data
- 39 Microarray
- 40 Other bioinformatics analysis
- 41 Supplemental Material
- 42 None of the aforementioned data types are in this research article
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
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)
