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Een paar dingen:
* Tomcat-dev is een paar keer herstart, mijn excuses als iemand daar last van heeft gehad. Het was ongepland.
* Onder tomcat-dev/webapps zijn ‘remotetaverna.war’ en remotetaverna erbij gekomen
* In catalina.policy is een regel gezet om voor de database die bij remotetaverna hoort (Edgar, misschien wil je die bekijken).
* Die database staat in /home/aida/remoteTavernaDB
* Login is admin en wachtwoord is geheim, maar het liefst je eigen naam en wachtwoord aanmaken
* De runner is op adres: http://aida.science.uva.nl:9999/remotetaverna/v1/
* Op myExperiment heb ik alvast een ‘runner’ aangemaakt: http://www.myexperiment.org/runners/5

• 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.

• The list output combines the ‘B-Protein’ and ‘I-Protein’ of the other output formats
• The resulting names are often more than a gene symbol (e.g. ‘NRG1 gene’)
• Sometimes a B-Protein is truncated and a gene symbol extension is the first I-Protein (e.g. ‘DNAse’, ‘I’)
• B-Proteins can have little mistakes (e.g. ‘STA1,’), with regexp I clear comma’s and points at the end of B-Proteins
• Conclusion: I do everything: list output (B-Protein+I-Protein), B-Protein only (with and without [,.]) before validation

I tested applyCRF with Matijn Schuemie’s UniProt service. The purpose is to filter our false positives. I found that

• Many proteins names give no result; these are generally not human (Scheumie’s service is human only)
• The DDBJ service, GetGene_DDBJentry or GetProd_DDBJentry from Japan can also be used
  • works on many organisms
  • multiple results: from which organism is the extracted protein name?
  • more unique names could be retrieved if the organism is know
• Conclusion: organism is essential to identify a protein name: a gene symbol is (more or less) unique within a species. Add organism name to document search? What to do when id is not unique?

ToDo

• Compare NER and applyCRF in one workflow
• Consider taking up organism name in document search query.

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