dictyBase SOPs: Curation Tools
Return to SOPs Index

Curation Tools

Last updated April 28, 2006
Colleagues Process colleague forms
Feature Curation Curate Gene
Curate Feature
Load GenBank Records
Literature Curate Literature
Reference Search
Link a PubMed Reference
GO and Phenotype Curate GO
Curate Individual Phenotype
Curate Strains
GO Obsolete Term Report
Update Dicty Phenotype and Mutant Types Ontology
Paragraphs Load Paragraph
View Blast Reports
Genome Update View Changed Curated Models

Process Colleague Forms [TOP]
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 [TOP]
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.

  • 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.
  • 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: Enter all published gene name synonyms in this field. Be sure to reference a publication or personal communication in the Notes field.
  • 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: 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.
  • 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: This field is fully free-text. Enter and edit in the box provided; this field can also accept html tags.
  • 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 Feature [TOP]
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.
  • To modify the coordinates of a Curated Model, load the Curated Model in Apollo.

Load GenBank Records [TOP]
New GenBank records are imported automatically on a weekly basis. Check the GenBank Loader weekly to see if new records are in the database. See the criteria for reconciling GenBank records with a Gene Prediction.

dictyBase curator:
  • Check to see that the GenBank record is aligning with the correct gene.
  • Check all information for accuracy and compatibility with existing information in the database.
  • Click 'Load' and information will be available on production.

Curate Literature [TOP]
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 [TOP]
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 [TOP]
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.

Curate GO [TOP]
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 [TOP]
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. Be sure to consult the Phenotype Ontology for new phenotypes.

  • Use the "Search existing phenotypes" tool to see if the gene product you are assigning already exists. If you conform to existing phenotypes, it will reduce the number of redundant phenotypes in the database. If the appropriate phenotype does not exist, it is of course acceptable to add a new one. Alternatively, while the number of phenotypes is relatively small, you can browse phenotypes with a simple SQL:
    select phenotype, phenotype_no from phenotype order by phenotype;
  • To add: fill in the following fields:
    1. Choose Mutant/Phenotype Type (Null, TS, CS, Overexp, Sys Del, Synthetic/multiple, Other)
    2. Enter Phenotype (If phenotype exists, enter phenotype_no, otherwise enter a new phenotype in the large box)
    3. Enter Sentence (Sentence optional; parent strain mandatory, for example [parent: AX2] or [parent: unavailable])
    4. Reference_no OR PubMedID
    5. Enter loci that share this GO annotation (optional)
  • To modify: the phenotype can be modified directly in the box; in this case a new Phenotype_No will be created (this should be avoided if possible). References and sentences can be modified directly in the Reference box; in that case a dictyBase reference_no must be provided.
  • To delete: check the delete box on the right. Do not check the "Delete the phenotype from the database" box if the phenotype is shared by other genes.

Curate Strains [TOP]
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 [TOP]
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 [TOP]
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.

Load Paragraph [TOP]
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/>
    • Entities: see W3 Schools list of HTML Entities. To use an html entity, add &amp; to the beginning of any html entity:
      &amp;micro; displays ยต on the screen
    • Gene Names:
      <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.
  • Click on 'Search Genes' to associate the summary paragraph to additional genes.

Internal BLAST [TOP]
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 Report [TOP]
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.

View Changed Curated Models [TOP]
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.

Home| Contact dictyBase| SOPs| Site Map  Supported by NIH (NIGMS and NHGRI)