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.
|“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 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
- all gene links within genomic expressions will be unmade