caifand
commented
5 years ago Several responses here:
- But we do have people's name as
creator. And that's the part we definitely want to keep, for giving credit to the actual software creators. Is there any automatic way to distinguishpublisherfromcreator? (I can think of matching organization entity names via arcGIS API but that would cost some time.) - I did notice some papers in which software is not named accurately by authors. But I think such cases are rare and if they really deteriorate the dataset quality how about just dropping them?
- The way to annotate non-continuous software names is very cool. Is it something can be done automatically or it will need more input from the training set?
- I still think subroutines should be separately coded given that there are usually separate creators associated with them. This including both packages in R or command in MATLAB. i.e., in either case, there should be two mentions being coded, in my opinion. (in response to one of the points in #637 as well)
kermitt2
Here are some remaining issues we observed in the current annotation scheme:
we kept so far the type name
creator, but actually we almost always have here the "publisher" of the software, having a person name is exceptional. We could thus use ratherpublisheras name for this annotation, given than annotated entities have not always created the software but simply commercialize it (for instance IBM is not the creator of SPSS, it has acquired SPSS Inc.).Sometimes, the name of the software publisher are used to refer to a software (PMC3534176):
MathWorks is the company developing MATLAB (the correct name was introduced at the beginning of the paper, but a strange shift in referring expressions happened in the middle of the paper!). It is hard to decide how to annotate this case.
We leave "MAS5" (the acronym of "Affymetrix microarray suite") unannotated while it could be valuable for disambiguation. Currently software name are always considered as a continuous chunk.
As an improvement, we could use non-continuous software name annotation like this:
We observed this case as encoded as another software entity (as above first example), sometimes both together in one, sometimes only the framework is annotated (as above second example). This case is not frequent and we have not fixed an annotation rule for this yet.
However we have not considered for the moment the "GraphPad Prism" case, where the name of the software is actually Prism and its editor is GraphPad, so it should normally be annotated like the "Microsoft Excel" case.
Similarly "Lotus Notes" is always identified as such, and not as "notes" from Lotus Inc. (although it is now called IBM Notes, but it's another story). So here unconsistencies remain for the moment.