Help:TFCatWiki FAQ

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[edit] Do I need to log on to TFCatWiki?

You need to log in if you wish to contribute to a gene's discussion page. You can browse and search the wiki without logging in.

[edit] How do I log on to TFCatWiki?

You can create a user name and password using the link at the far right corner of each page. Once you've created a user you can log on using the same link.

[edit] Why can't I log on with my wiki user id and password?

If you are having trouble logging on, it may be because the MediaWiki software capitalizes your user id name. Please ensure that you capitalize the first letter of your user id when entering your user id at the user log on prompt. If you have lost or forgotten your password, you can request that a password change process be initiated at the user log on prompt.

[edit] Why do some genes have annotations from more than one reviewer?

During our annotation review process, multiple reviewers performed annotations on the same set of genes for the purpose of discussing and establishing standardized annotation formats and content. We also conducted a random, blinded quality assurance analysis of the annotations, which required assignment of genes, which had already been annotated, to another reviewer. Lastly, we assigned the same set of genes to a group of annotators to conduct annotation training. In general, each gene will have at least two pieces of evidence collected from one or more journal articles.

[edit] Why do some gene annotations with multiple reviewers disagree on judgement or taxa assignment?

Annotations are based on the journal evidence reviewed. We did not perform an exhaustive review of all journal article evidence for a gene. Therefore, some reviewers chose different articles to review the same gene and made an assessment based on the evidence presented in these articles. Reviewers reviewing the same gene have endeavored to align their judgements into positive (a TF), negative (not a TF), and indeterminate judgement categories. A gene may belong to multiple functional taxa.

[edit] Are TFCat entries primarily indexed by the mouse or the human GeneID?

Mouse. If we have identified a human ortholog, a link to the human GeneID is provided with the entry. Human TF genes with no mouse ortholog were not included in the first release of TFCat.

[edit] How should I quote the gene annotation reviewer comments text?

The reviewer TF summaries can be quoted directly. In annotations specifically related to scientific articles (as indicated by an associated PubMed article identification number), the text may include quotations from the paper. Contributing annotators followed diverse practices in how they formatted these entries. We encourage the users to refer back to the original papers if they intend to make a specific quotation of this information.

[edit] How do I provide feedback about an annotation?

If you wish to provide feedback about a particular gene annotation, please use our feedback tracking system available [here] See the Feedback Tracking Help for more information and access to help.

[edit] Why do you have an e-mail notification system extension and how is it different than the Watch function?

The gene annotation (article) page is not modifiable through the wiki. On occasion, the wiki gene page may get updated through our TFCat Annotation Feedback System workflow. You may use the watch and watchlist wiki functions to receive individual e-mail notifications about changes to a particular wiki gene page. Alternatively, our e-mail notification system extension provides a summary list of gene pages that have been modified within a specified notification period. You can opt into (or out of) one or both e-mail notification systems. To setup a watchlist, please change your 'preferences'. To modify your extended (summary level) e-mail notification parameters enter your wiki user id and password here.

[edit] How do I link to a TFCatWiki gene page?

You can link to the gene page using either the gene symbol_gene id or MGI id or HGNC id. For example, any of the following urls: http://sonoma.cmmt.ubc.ca/TFCatWiki/index.php/sox2_20674 or http://sonoma.cmmt.ubc.ca/TFCatWiki/index.php/MGI:98364 or http://sonoma.cmmt.ubc.ca/TFCatWiki/index.php/HGNC:11195 will take you to the Sox2 gene page.

[edit] How do I download TFCatWiki data?

You may download the data at www.tfcat.ca.

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