Curation Tools

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Contents

Colleagues

Process colleague forms

Description
Here you can manually update colleague information by colleague_no, or commit changes or new entries that colleagues have entered themselves.
dictyBase curator
Check this at least once a day to see if any colleagues have been added, or if colleagues have edited their information.
IMPORTANT: Any changes made in this page will be e-mailed to the colleague. For entering genes associated with the colleague, use the Gene Curation Page.
To change colleague information manually:
  • You will first need to find the colleague_no. To do this, search for the last name of the colleague on the Colleague Submission/Update form. Click 'EDIT' for the appropriate colleague and take note of the ID number; this is the colleague_no.
  • To manually change any colleague entry, click 'Delete or Update Colleague Info by Colleague_no.'
  • To delete a colleague, click 'Delete.' To make changes, click Update.
  • In the next page, make any necessary changes and hit Submit.
To update colleague submissions:
  • To update changes that colleagues have entered themselves, click on the 'MajorUpdate' link.
  • Here you can view the new information that a colleague has entered and check for irregularities or typos. Also make sure they have entered the names of their colleagues correctly. Failure to do so will create extra entries for colleagues who already have an entry.
  • If everything checks out, hit Submit. The new information will then be committed to the database and appear online.


Curate Gene Information

Description
From the Gene Curation Page, it is possible to curate most fields that appear on the Gene Page. It is also possible to curate the sequence features that are associated with the gene from this page.
dictyBase curator
When entering new information in the Gene Curation Page, most of the fields are 'free text.' After entering information and hitting 'Commit,' be sure to refresh the Gene Curation Page if you return. Failing to do so could result in loss of information.

Gene Name

  • The Gene Name may be changed by overwriting the old name with the new name. This is case-sensitive so be careful! See also Procedure for naming genes.

Deleting a gene

  • To delete a gene, check the box 'Deleted?'. The gene will still exist in the database but it will not be present on production.

Synonym

  • Synonym: Enter all published gene name synonyms in this field. Be sure to reference a publication or personal communication in the Notes field.

Protein Synonym

  • Protein synonym: Enter all published protein name synonyms in this field. Be sure to reference a publication or personal communication in the Notes field.

Gene Product

  • Gene Product: Because gene products are an important part of the dictyBase Search on production, it is necessary to be as consistent as possible with Gene Products. Click 'Search gene product' and a new window pops up. Enter all or part of the Gene Product and use the check boxes to enter existing Gene Products on the Gene Curation Page. If you must create a new Gene Product, try to be consistent with existing Gene Products. We are DISCUSSING TO CHANGE GENE PRODUCT ANNOTATIONS. See Gene Products.

Researchers

  • To add Researchers, click on 'Search Colleagues' and use check boxes in search window to enter colleagues on the Gene Curation Page. This is the preferred way to add a dictyBase colleague as adding a colleague to a gene using the Colleagues tool sends an Email to that colleague. See Guidelines for associating researchers and genes.

Description

  • Description: This field is fully free-text. Enter and edit in the box provided; this field can also accept html tags.
  • Community annotations in Description:
    • add tag:
       <b>Community annotation:</b> 
    • keep the length to about 10 lines of text.
    • link back to the wiki page:
       <a href="http://wiki.dictybase.org/dictywiki/index.php/ ... "> There is more information on the wiki page</a> 
    • add user name :
       <br/> <i> username, Date </i>

Name description

  • Name description: In this field, spell out the acronym for the gene name. Make a note of the reference from which the description was derived in the notes field. Use html tags to make letters bold, for example:
sad = <b>S</b>ubstrate <b>AD</b>hesion
  • Features: Click 'Edit' for a particular feature to edit information and create Curated Models. See also Curate Feature.
  • GO: Click on 'Curate GO' to open up the GO Curation Page. See also Curate GO for more information.
  • Phenotype: Click on 'Curate Phenotype' to open up the Phenotype Curation Page. See also Curate Individual Phenotype for more information.
  • Strains: Click on 'Curate Stock Center Strains' to open up the Stock Center Curation tools. To edit a strain, search for it on the Strain and Inventory Search Page. To add a new strain, click 'Add a new strain' in the left menu. Enter all relevant information and hit 'Submit.'
  • Literature: Clicking on 'Curate Literature' will open a new window with all curated and uncurated references associated with the gene. See also Curate Literature for more information.
  • Paragraph: Using this tool, a paragraph may be added to the gene plus additional genes. See Load Paragraph for more information.
  • Notes: Public and private Notes can be created. Use the check box to indicate public/private. To change a note, click 'Edit' or 'Delete.'



Curate Sequence

Description

The Feature Curation tool can be used to create a Curated Model (from the Sequencing Center Gene Prediction) and delete or check off evidence for a Curated Model.

dictyBase curator
  • If accessed through dictyBase Curator Central, enter the dictyBaseID for the feature you'd like to curate.
  • From the Gene Curation Page, select 'Edit' and a new window opens.
  • Sequencing Center Gene Prediction: To create a Curated Model that is a duplicate of the predicted gene model, click 'Create dictyBase Curated Gene.' The Curated Model is a new feature with a new dictyBaseID. A new window will give you the option to further curate the old feature or the new feature.
  • Curated Model: Use the Feature Curation page to check off the evidence used to support the Curated Model. To remove the feature from production, click 'Deleted?' and enter a 'Replaced by (dictyBaseid) if possible.
  • Check All That Apply:
  • Incomplete support: used when support does not exist for the full coding sequence.
  • Pseudogene: check this box when evidence points to the gene being a pseudogene.
  • Changed: only used by developers.
  • Conflicting evidence: check this box when two pieces of conflicting evidence exist (for example, ESTs and genome sequence).
  • Derived from:
  • Sequencing Center Gene Prediction: automated gene prediction.
  • gene sequence: GenBank genomic sequence.
  • curator inference: gene model comes from curator's brain.
  • Supported by:
  • mRNA: GenBank mRNA sequence.
  • ESTs: sequences from the cDNA project.
  • sequence similarity: similarity with other protein/DNA sequences.
  • unpublished cDNA: cDNA sequence provided by a researcher but not available in GenBank.
  • To modify the coordinates of a Curated Model, load the Curated Model in Apollo.




Load GenBank Records

see Service_Week_Tasks

Literature

Curate Literature

Description
This tool allows curators to associate Literature Topics to a paper in a gene-centric way.
dictyBase curator
  • Enter the gene name of the gene for which you'd like to curate literature.
  • Select 'Curated PubMed References' or 'New PubMed References Not Yet Curated.' Additional curation can always be done to a curated publication.
  • At the top left of the page, you can add additional genes to the reference. Enter gene names and click on 'Add Loci and Curate.'
  • At the top right of the page, you are given options for unlinking. Scroll to the bottom of the page and hit 'Submit' to make these changes.
  • Use the check boxes to associate Literature Topics for the gene. If you would like to associate the same Literature Topics with other genes associated with the reference, enter those names in the 'shared by' box and click 'Submit.'




Reference Search

Description
Using this tool, you can search for references in the database. Search for PubMed ID (PMID), citation (Volume, Page number), or by authors and keywords (none of which can be searched on production). You may also restrict the year of publication.




Link a PubMed Reference

Description
Using this tool, you can link any PubMed reference to any gene in the database.
dictyBase curator
  • Enter gene name where it says 'Locus or locus_no.'
  • Enter a PubMed ID. The PubMed reference must already exist in the database.



GO and Phenotype

Curate GO

Description
See GO Documentation and dictyBase Gene Ontology Help.
dictyBase curator
Determine the best GO terms for the gene product based on literature and/or sequence similarity.
  • Find GO terms using OBO-Edit and/or AmiGO.
  • To add Gene Ontology annotations, fill in the following fields:
  1. Ontology (Process, Function, or Component)
  2. Enter GO ID number (GOid)
  3. Qualifier (NOT, colocalizes_with, or contributes_to)
  4. Reference_no OR PubMedID
  5. Evidence Code (IDA, IEA, IEP, IGI, IMP, IPI, ISS, NAS, ND, TAS; see also dictyBase Evidence Codes)
  6. With OR From Association (Use with IGI, IPI, ISS, IEA Evidence Codes; enter DB:id) OR IC from GOid (enter GOid that is also annotated to the gene)
  7. Enter genes that share this GO annotation (optional)
  • To delete: check the "delete" box for the particular GO annotation you want to delete.
  • You MUST annotate all 3 ontologies (Process, Function, Component), even if it is "unknown" (ND = No Data).
  • See also the dictyBase guidelines for GO annotation for more detailed Gene Ontology SOPs.




Curate Individual Phenotype

Description
Phenotypic characterization as described in the literature.
dictyBase curator
Determine phenotypic information from all available literature. We do not accept phenotypes via personal communication; all phenotypes must have a published reference. Use Phenotype Ontology terms for phenotype annotations. To add a phenotype annotation, fill in the following fields:
  1. Choose Mutant/Phenotype Type (select from drop-down menu)
  2. Phenotype Ontology ID (Search the ontology term or enter an ID if you know it)
  3. Enter Sentence (add parental strains and strain names when possible)
  4. Enter reference_no or PubMedID
  5. Enter genes sharing this phenotype




Curate Strains

Description
This link takes you to the Dicty Stock Center curation pages.
dictyBase curator
The Stock Center curation pages allow you to add and modify information in strain records.
  • Add strain name and synonym, description, genotype, etc.
  • Add PubMed reference by PMID.
  • Guidelines for strain curation?




GO Obsolete Term Report

Description
This is a table generated by the programmers to notify curators when a dictyBase gene product is annotated to an obsolete GO term. The table contains the GO ID of the term, the Locus_No of the dictyBase gene, the date the association was made, and who made the annotation. In some cases, it is an IEA (inferred by electronic annotation) and was not created by a curator.
dictyBase curator
Obsolete GO terms should not be annotated to gene products.
  • To delete the obsolete GO term, click on the Locus_No, which directs you to the GO Curation Page for that gene.
  • Mark the offending term's 'delete?' box and hit 'Submit.'
  • If possible, the term should be replaced. Look for new or suggested terms by downloading the latest geneontology.obo file or with AmiGO.




Update Dicty Phenotype and Mutant Types Ontology

Description
This tool loads the current version of the phenotype ontology (dicty_phenotypes.obo) and mutant type ontology (mutant_types.obo) into the database.
dictyBase curator
For instructions for editing and loading the ontologies, click here.



Paragraphs

Load Paragraph

Description
This tool allows curators to add a gene summary paragraph to a gene or to multiple genes.
dictyBase curator
Write an XML file using approved tags. Summary paragraph should include most important facts about the gene or gene family and link to other relevant genes, Gene Ontology terms, and references.
  • XML tags:
  • General tags:
<b> bold </b>; <i> italic </i>; <u> underline </u>; line break <br/>
&micro; displays ยต on the screen
  • Gene Names:
<locus gene_id='' name='' /> 
<locus name="abcD"/>
  • References:
<reference pmid="15496465">Authors (YEAR)</reference>
<reference reference_no="9985">Authors (YEAR)</reference>
  • Gene Ontology terms:
<go id="8976"/>
  • Insert XML file between the tags.
<summary></summary>
  • Click on 'Search Genes' to associate the summary paragraph to additional genes.

BLAST

Internal BLAST

Description
This BLAST Server is identical to the one on production, however, you may BLAST against databases not found on production. Examples of other BLAST databases include SwissProt, GO protein database, and gene predictions not yet available on production.
dictyBase curator
As on production, select a program to run (blastn, blastp, etc.), paste your sequence in FASTA format, select a database against which to BLAST, set parameters, and hit 'Run BLAST.'




View Blast Reports

Description
This is a place where the programmers can store high-throughput BLAST reports. Curators can view reports, which have links to dictyBase Gene Pages.
dictyBase curator
BLAST reports are named by subject vs. query and the date in the form MMDDYYYY.
  • Click on a BLAST report and you will be directed to a page with a list of queries in the left-hand frame.
  • Click on a Query and the BLAST result will appear in the right-hand frame.
  • Click on a Hit and the alignment with that hit will appear in the right-hand frame.
  • Clicking on a dictyBaseID in the right-hand frame will direct you to the Gene Page for that feature.



Genome Update

View Changed Curated Models

Description
This is a place where the programmers can store information about changes in gene models during a genome update. Curators can view all changed genes, which have links to dictyBase Gene Pages. This page currently shows Version 2.5, updated in December of 2005.
dictyBase curator
Look at this page during a genome update.



return to SOPs Index

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