From mamandel@unagi.cis.upenn.edu Wed Aug 20 12:48:51 2003 Date: Wed, 20 Aug 2003 12:43:21 -0400 (EDT) From: Mark A. Mandel To: Oncology Named Entity Annotators List Subject: Notes from meeting of Aug. 19. NO MEETING NEXT WEEK I tried to get this mailing out last night, but unagi and all the internet links went down, probably because of the !@#$%^&* worms and viruses. Between yesterday and today I have deleted nearly 2,000 messages from my inbox that were either virus-laden mailings or notifications that a virus had been detected in "my" mailing to someone I'd never heard of (i.e., a virus had spoofed my return address as the source of the garbage). See end of this message for more info. I. ADMINISTRATIVE BUSINESS II. Discussions and decisions III. Appendix (Things I've done since the meeting) IV. THE SOBIG VIRUS -- Mark A. Mandel I. ADMINISTRATIVE BUSINESS 1. There will be no annotators' meeting next week; the closing on my house is at the same time, and we don't have many people around anyway. 2. Everyone please send your schedule information to Ramez for the fall term as soon as you have an idea of it. 3. Julie is back from her internship in D.C. Welcome back! Unfortunately, her computer fell victim to the Blaster worm, so she will be using the public computers at IRCS for a while. II. Discussions and decisions 1. Genes as locations When a gene is the object of a variation -- when the gene itself (rather than some part of it) is deleted, repeated, or moved -- we will tag it as BOTH Gene/RNA and Location. Example wordings and taggings: - deletion of the K-ras gene type---- G/RNA loc-- - translocation of the H-ras gene to location such-and-such type--------- G/RNA loc-- loc------------------- Other variation types that a gene can be a location for include - duplication - amplification (See http://www.cis.upenn.edu/~mamandel/annotators/WF-how-to.html#double-tagging for tips on the mechanics of double-tagging in WF.) This DOES NOT apply to expressions like "a deletion mutation in the K-ras gene at codon 5", where the variation is specified as affecting a nspecific section of the gene rather than the whole gene. We will continue to tag the gene separately in such expressions; its relation to other components of the variation event will be annotated at a later stage, entity and relation tagging: - a deletion mutation in the K-ras gene at codon 5 type---- G/RNA loc---- Similarly for expressions like "K-ras mutations", with little or no specific information about the location other than the gene. Tag a gene as both location and Gene/RNA *only* where it is clear that the variation affects the entire gene. - K-ras mutations G/RNA event---- 2. Genes within locations A location can be specified as a range, like "codons 18 through 20". And sometimes this range is stated in terms of genes: "from gene A to gene B", "between genes A and B", etc. In such cases, we will tag the range as a location AND we will tag the genes within it: - from gene A to gene B G/R G/R Loc-------------------- - between genes A and B G/R G/R Loc-------------------- 3. Multiple elements within a variation event Remember, in dealing with the above, that a single variation event may have more than one location: - at different scales ("base pair 35" and "codon 12") - because an element is moved ("t(11; 14)(q13; q32) chromosomal translocation") [specialists, how should we parse this?] There may be multiple original and altered states: A -> T, resulting in a change from glycine to alanine st-orig st-alt st-orig st-alt Even the type can be described in different ways: "loss of heterozygosity" (or "LOH"), "deletion", and simply "loss" may be used for the same event. III. Appendix Things I've done since the meeting: Added table of contents to the WF users' guide http://www.cis.upenn.edu/~mamandel/annotators/WF-how-to.html Enlarged and organized the Tips section http://www.cis.upenn.edu/~mamandel/annotators/WF-how-to.html#tips Fixed the gene-entity links from the oncology definitions page. IV. THE SOBIG VIRUS This is from our system administrator: >>>>> Folks, As many of you are aware by now, there is a new virus floating around the Internet. This one seems to be quite agressive in sending out mass e-mails. While the damage is categorized as "low", the distribution is quite high. Technical details: http://securityresponse.symantec.com/avcenter/venc/data/w32.sobig.f@mm.html Summary: The e-mail message will have the following characteristics: From: Spoofed address (which means that the sender in the "From" field is most likely not the real sender). The worm may use the address admin@internet.com as the sender. -------------------------------------------------------- Subject: Re: Details Re: Approved Re: Re: My details Re: Thank you! Re: That movie Re: Wicked screensaver Re: Your application Thank you! Your details Body: See the attached file for details Please see the attached file for details. Attachment: your_document.pif document_all.pif thank_you.pif your_details.pif details.pif document_9446.pif application.pif wicked_scr.scr movie0045.pif -------------------------------------------------------- If you receive such messages, please delete them right away. Most importantly, do *NOT* open the attachments. As a reminder, e-mails from CETS or manager@[system] will *never* contain an attachment or otherwise instructs you to open an attachment. The latest Norton Antivirus definition will automatically detect and remove/quarantine the above-mentioned virus. It is dated 8/19/2003, version 50819c. Thank you for your attention. Gilbert M. Kowie Systems Administrator IRCS - LDC - CIS <<<<< -- Mark A. Mandel