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2013-06-11: Alan Ruttenberg is in the process of doing a scripted translation of this work into OWL for the Immport project. --- From: Alexander Diehl <firstname.lastname@example.org> Date: Tuesday, June 11, 2013 8:52 AM To: Dave Dougall <David.Dougall@baylorhealth.edu> Subject: ImmPort Cell Ontology Hi Dave, Thanks for your help in talking to us last week. Alan Ruttenberg is working to add more of your curated information to the CL and wanted me to ask you a couple of things: 1) As you know, you provided Terry and me with a lot of additional information about cell type-marker associations as part of comments fields for particular cell terms. In preparing the same information for ImmPort, did you map the markers to Protein Ontology terms or was that performed by someone else? 2) What file did you provide ImmPort? Was it a modified cell.obo file, an Excel spreadsheet, or a tab delimited file? The reason Alan is interested in these things is that he wants to work directly from the information you provided so that his script to create necessary conditions that capture your curation efforts does not pick up errors that may have been introduced when the file you originally gave ImmPort was converted for display on the ImmPort website. It's not that Alan thinks there are errors, but he simply wants to work with the original file you provided just to be sure. Thanks, Alex ---- Alex, Sorry for some of my confusion last week. I hadn't done much work on the CL in the past year, only occasionally when I ran into an article of interest. It also would have helped if I would have had a heads-up as to what specific excel files there were questions about. Many of the files discussed came from me, but some seem to have been produced by NG. 1. Yes, I would generally map the markers to the Protein Ontology or GO. This was recorded in an excel spreadsheet that I created. In the CL comments field, I would only include the marker/cytokine terms (e.g. CD279, IL2, etc.), not the Protein Ontology ID. 2. I would provide them with an excel spreadsheet, such as the one attached (import_phenotype_v1.3). There was a color coding based on sub_category (Cytokine red font, Surface Maker blue font, transcription factor green font, etc.). Additionally, anything in red font is an update from the previous version of the file. I also began to include the experimental method used to determine + or – expression, which is important, but as you can see, not well populated. In another file, import_term_table_v1.2, I would curate all the terms used as to what category they belonged, Cytokine, Surface Marker, GO, etc. (also color coded, with red font indicating a new term from the previous version of the file). Also for your viewing pleasure, I included a presentation I did for a lab meeting w/ Richard Scheuermann's group at UTSW. This gives information on some problems we had and plans to do, many of which you are well aware of. Enjoy. Dave