Difference between revisions of "Markup excerpts"

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==GSA markup==
back to [[Pipeline for markup | GSA markup SOP]]<br>
*[[Pipeline for markup]]
back to [http://www.wormbase.org/wiki/index.php/Milestones_and_progress Entity classes and problems]<br>
*[http://www.wormbase.org/wiki/index.php/Milestones_and_progress Entity classes and problems]
[http://textpresso-dev.caltech.edu/gsa/worm/html/ Marked up html index]
**[[Papers that have been markedup]]
**[[Markup excerpts]]
==Classes and problems==
==Classes and problems==
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Latest revision as of 21:29, 23 July 2013

back to GSA markup SOP
back to Entity classes and problems
Marked up html index

Classes and problems


This is an example of text markup testing the feasibility of linking based on anatomy_name. As you will see, there are a number of problems with the links that are created.

Markup excerpt 1.jpg

Problems encountered when linking anatomy_names
Anatomy_name Problem Possible solution
“set”, “cell” Real term but also common word Make context specific
“CAN” Real term but also common word Use case sensitivity
“AC”, “FLP” Real term but also different meanings “… (<AC>pAC> < 0.001) and 0.95 (<AC>pAC> < 0.001) in wild-type” AC is not anchor cell “e.g., the FLP recombinase system (Davis et al. 2008).” FLP is not neuron cell Manual correction…context specificity?
“organism”,“organ”, “axis”, “neuronal”, “head”, tail” Too general for the researcher? Remove from list?
“PhaA/B”, "CAN", "VPC" Synonyms not recognized: “CSN” for ciliated sensory neuron, “VPC”s for vulval precursor cells, “PhaA/B” Add to entity list
“neuron” okay, “neurons” not okay Plurality problems Make plural indifferent
“Lateral sense organ”, “P12 ectoblast” not linked Term not on list: "P12" ok but the expression "P12 ectoblast" isn’t, Synonym problem?? Add term? Add synonym? Just omit for linking?
Single letters “D”, “K”, etc Too many false hits: Protein domains “C terminus”, “D domain", Figure panel references “in panel A of Figure 1” Remove single letters from list, or make context specific.

Genomic Expressions

Genomic expressions are not correctly linked
It is not correct to link transgene expressions to the individual entities within the construct

Genexpression bad link.jpg

*Note: This genotype is hidden from web page in the tag General_remark, same as for other plasmids ex. HSP-FLP1, pRF4, cpjM1HG.11, IM#171, p76-16B, pPD118.33, pTG96, etc.

Genomic expressions.jpg

  • Common name is genotype, not actual name:
    • ttx-3p::GFP, in this case, the transgene is mgIs18, but not stated as such in the paper. The expression “[ttx-3::GFP]” in the Summary of mgIs18 in acedb
    • sur-5::GFP
  • Solution:
    • all gene links within genomic expressions will be unmade