Clean up of archive: keywords

[Melissa37]

eg differences: e.coli E.coli E. coli e. coli E. Coli <italics>E. coli</italics>

etc

There are others too. I'll ask Sian/Nathan for the database info so we in editorial and production can start working out the extent of the problem!

[Melissa37]

https://docs.google.com/spreadsheets/d/1LlVtROqJZ2s_sgtCMDco725aeGf5LXIQrtHflVptpbE/edit?pli=1#gid=2066109275

[gnott]

First draft conversion of the archive is ready to roll. The strategy is to convert the value to lower case (and remove any italic tags), and then look for a match from the following list. If there's no match, then the original XML is used. This is used to replace the existing tag.

Python match dict below:

        match_list['arabidopsis'] = '<kwd><italic>Arabidopsis</italic></kwd>'
        match_list['b. subtilis'] = '<kwd><italic>B. subtilis</italic></kwd>'
        match_list['c. elegans'] = '<kwd><italic>C. elegans</italic></kwd>'
        match_list['c. intestinalis'] = '<kwd><italic>C. intestinalis</italic></kwd>'
        match_list['chicken'] = '<kwd>Chicken</kwd>'
        match_list['ciona intestinalis'] = '<kwd><italic>C. intestinalis</italic></kwd>'
        match_list['d. melanogaster'] = '<kwd><italic>D. melanogaster</italic></kwd>'
        match_list['dictyostelium'] = '<kwd><italic>Dictyostelium</italic></kwd>'
        match_list['drosophila melanogaster'] = '<kwd><italic>D. melanogaster</italic></kwd>'
        match_list['e. coli'] = '<kwd><italic>E. coli</italic></kwd>'
        match_list['frog'] = '<kwd>Frog</kwd>'
        match_list['fruit fly'] = '<kwd><italic>D. melanogaster</italic></kwd>'
        match_list['human'] = '<kwd>Human</kwd>'
        match_list['macaca mulatta'] = '<kwd><italic>M. mulatta</italic></kwd>'
        match_list['maize'] = '<kwd>Maize</kwd>'
        match_list['mouse'] = '<kwd>Mouse</kwd>'
        match_list['myceliophthora thermophila'] = '<kwd><italic>M. thermophila</italic></kwd>'
        match_list['n. crassa'] = '<kwd><italic>N. crassa</italic></kwd>'
        match_list['neurospora'] = '<kwd><italic>Neurospora</italic></kwd>'
        match_list['none'] = '<kwd>None</kwd>'
        match_list['oncopeltus fasciatus'] = '<kwd><italic>O. fasciatus</italic></kwd>'
        match_list['other'] = '<kwd>Other</kwd>'
        match_list['plasmodium falciparum'] = '<kwd><italic>P. falciparum</italic></kwd>'
        match_list['platynereis dumerilii'] = '<kwd><italic>P. dumerilii</italic></kwd>'
        match_list['rat'] = '<kwd>Rat</kwd>'
        match_list['s. cerevisiae'] = '<kwd><italic>S. cerevisiae</italic></kwd>'
        match_list['s. pombe'] = '<kwd><italic>S. pombe</italic></kwd>'
        match_list['salmonella enterica serovar typhi'] = '<kwd><italic>S. enterica serovar</italic> Typhi</kwd>'
        match_list['streptococcus pyogenes'] = '<kwd><italic>S. pyogenes</italic></kwd>'
        match_list['viruses'] = '<kwd>Virus</kwd>'
        match_list['volvox'] = '<kwd><italic>Volvox</italic></kwd>'
        match_list['xenopus'] = '<kwd><italic>Xenopus</italic></kwd>'
        match_list['yellow baboon (papio cynocephalus)'] = '<kwd><italic>P. cynocephalus</italic></kwd>'
        match_list['zebrafish'] = '<kwd>Zebrafish</kwd>'

[gnott]

Updated list - added 'bat', changed arabidopsis, macaca mulatta, salmonella enterica serovar typhi

        match_list['arabidopsis'] = '<kwd><italic>A. thaliana</italic></kwd>'
        match_list['bat'] = '<kwd>Bat</kwd>'
        match_list['b. subtilis'] = '<kwd><italic>B. subtilis</italic></kwd>'
        match_list['c. elegans'] = '<kwd><italic>C. elegans</italic></kwd>'
        match_list['c. intestinalis'] = '<kwd><italic>C. intestinalis</italic></kwd>'
        match_list['chicken'] = '<kwd>Chicken</kwd>'
        match_list['ciona intestinalis'] = '<kwd><italic>C. intestinalis</italic></kwd>'
        match_list['d. melanogaster'] = '<kwd><italic>D. melanogaster</italic></kwd>'
        match_list['dictyostelium'] = '<kwd><italic>Dictyostelium</italic></kwd>'
        match_list['drosophila melanogaster'] = '<kwd><italic>D. melanogaster</italic></kwd>'
        match_list['e. coli'] = '<kwd><italic>E. coli</italic></kwd>'
        match_list['frog'] = '<kwd>Frog</kwd>'
        match_list['fruit fly'] = '<kwd><italic>D. melanogaster</italic></kwd>'
        match_list['human'] = '<kwd>Human</kwd>'
        match_list['macaca mulatta'] = '<kwd>Rhesus macaque</kwd>'
        match_list['maize'] = '<kwd>Maize</kwd>'
        match_list['mouse'] = '<kwd>Mouse</kwd>'
        match_list['myceliophthora thermophila'] = '<kwd><italic>M. thermophila</italic></kwd>'
        match_list['n. crassa'] = '<kwd><italic>N. crassa</italic></kwd>'
        match_list['neurospora'] = '<kwd><italic>Neurospora</italic></kwd>'
        match_list['none'] = '<kwd>None</kwd>'
        match_list['oncopeltus fasciatus'] = '<kwd><italic>O. fasciatus</italic></kwd>'
        match_list['other'] = '<kwd>Other</kwd>'
        match_list['plasmodium falciparum'] = '<kwd><italic>P. falciparum</italic></kwd>'
        match_list['platynereis dumerilii'] = '<kwd><italic>P. dumerilii</italic></kwd>'
        match_list['rat'] = '<kwd>Rat</kwd>'
        match_list['s. cerevisiae'] = '<kwd><italic>S. cerevisiae</italic></kwd>'
        match_list['s. pombe'] = '<kwd><italic>S. pombe</italic></kwd>'
        match_list['salmonella enterica serovar typhi'] = '<kwd><italic>S. enterica</italic> serovar Typhi</kwd>'
        match_list['streptococcus pyogenes'] = '<kwd><italic>S. pyogenes</italic></kwd>'
        match_list['viruses'] = '<kwd>Virus</kwd>'
        match_list['volvox'] = '<kwd><italic>Volvox</italic></kwd>'
        match_list['xenopus'] = '<kwd><italic>Xenopus</italic></kwd>'
        match_list['yellow baboon (papio cynocephalus)'] = '<kwd><italic>P. cynocephalus</italic></kwd>'
        match_list['zebrafish'] = '<kwd>Zebrafish</kwd>'

[gnott]

Ok to close this @Melissa37 ? I'm just going through looking at issues assigned to me and not closed.

[Melissa37]

Yup, thanks