Difference between revisions of "Markup excerpts"
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[http://www.wormbase.org/wiki/index.php/Milestones_and_progress GSA markup] | [http://www.wormbase.org/wiki/index.php/Milestones_and_progress GSA markup] | ||
− | =Classes and problems= | + | ==GSA markup== |
− | ==Anatomy_name== | + | *[[Pipeline for markup]] |
+ | *[http://www.wormbase.org/wiki/index.php/Milestones_and_progress Entity classes and problems] | ||
+ | **[[Papers that have been markedup]] | ||
+ | **[[Markup excerpts]] | ||
+ | |||
+ | ==Classes and problems== | ||
+ | ===Anatomy_name=== | ||
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. | 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. | ||
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− | ==Genomic Expressions== | + | ===Genomic Expressions=== |
Genomic expressions are not correctly linked<br> | Genomic expressions are not correctly linked<br> | ||
'''It is not correct to link transgene expressions to the individual entities within the construct'''<br> | '''It is not correct to link transgene expressions to the individual entities within the construct'''<br> |
Revision as of 19:17, 3 February 2010
GSA markup
Classes and problems
Anatomy_name
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.
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
*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.
- 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
- Possible solutions:
- make a link based on a query of the summary tag of a transgene object
- use the genotype as a synonym for the transgene object itself