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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.

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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.

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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

• Solution:
  • all gene links within genomic expressions will be unmade