SEED Viewer Manual/EditLiterature

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Revision as of 16:39, 4 December 2008 by DanielaBartels (talk | contribs) (Curating literature in SEED)

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Edit Literature

This page allows you to edit direct literature (dlits) for a feature. The tool automatically queries PubMed for Aliases of the feature ID to get candidate literatures for your feature.

CDS Info

This section displays a table with general information for the feature that might be valuable for deciding if a literature reference is relevant for the feature.

Requesting relevant publications from PubMed

This section displays publications that are not yet curated, as well as publications that are already assigned to be relevant or not relevant to the function of the feature. The literature references appear in the following tables:

Not yet Curated relevant publications:

These are publications the tool has identified as possibly relevant for the feature. You will get a checkbox in the first column of the table. Check the publications you want to assign as supporting the functional assignment of the feature, and press the button Save to relevant pmids underneath the table to save them as dlits.

Not yet curated publications (dlits):

Same as above, but the literature references were pre-computed.

Current DLITS for this gene:

This table shows all publications that are assigned to support the functional assignment of the feature (to be dlits).

Curated to be RELEVANT, but NOT DLITS:

Literature that is relevant, but not a dlit is literature that does not support the functional assignment to the feature, but refer to the genomic region the feature is in or give other information about the feature.

Curated to be GENOME PAPERS, not dlits:

These are references that refer to the whole genome of the feature or a genomic region, not directly the feature itself. Mostly, these papers deal with the sequencing process of the genome.

Curated to be NOT RELEVANT publications:

Not relevant publications.

Curating literature in SEED

Curation of the literature can be done two ways:

1) Add additional publications for this peg

You can manually add publications that have not appeared in any of the tables above. If you want to add more than one PubMed reference, separate them with a space. Press Save to relevant pmids to save the entered publications as supporting the functional assignment of the feature (dlit).

2) Drag and drop the PMID to the appropriate containers.

The categories for the publications described above can be found as containers in this section. The literature boxes in the containsers can be dragged and dropped from one container to another. This way, you can move any of the literature references to any container. If you have made your selection, press Save to attributes to save your selection.