I would like to limit the search results for the following related reasons:
- Protein names are not unique between organisms. They are closer to unique within an organism. Hence, if I could limit the search to papers e.g. in the human context, I would be more certain of the meaning of a protein name.
- Martijn Scheumie’s uniprot service that I use for validation works on human uniprots only. Without limiting the documents to search, it is more likely that I will erroneously instantiate a protein with a human uniprot id, while it is e.g. a yeast protein.
- More extracted proteins would be valid human proteins if I could preselect papers on organism.
mesh does not seem a solution:
- mesh headings include ‘organism’, but in my very rough survey it seems this categorisation is not always used. Many papers returned by ‘EZH2′ that are at least relevant to human cell biology are not tagged with ‘Humans’ or any organism.
adding ‘human’ and synonyms to the search query (i.e. not only mesh) is not a solution
- abstracts do not necessarily contain a reference to the organism in which context it is written (experts can tell or it is not so important for expert readers).
concept profiles could be useful
- A concept profile might be indicative of the organism the paper is about.