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  • ** AmiGO 2.1 release, looking at Drupal to cloud. Rama should check with Mike on Cloud solution. * Rama/Rachael:
    3 KB (524 words) - 15:00, 22 May 2014
  • Ben, Rama, Jane, Val, Eurie, Seth, Amelia
    956 bytes (140 words) - 09:35, 18 May 2010
  • 2. Rama: We have a question about the use of 'colocalizes with' qualifier. We are c 5. Rama: Ribosomal proteins
    7 KB (1,170 words) - 10:00, 12 August 2008
  • ...><span style="font-weight:bold;font-family:'Helvetica-Bold';color:#ec0003">rama: </span><span style="font-family:'Helvetica'">hello</span></p> ...><span style="font-weight:bold;font-family:'Helvetica-Bold';color:#ec0003">rama: </span><span style="font-family:'Helvetica'">i was happy with #2. Did ever
    30 KB (3,813 words) - 19:09, 29 February 2008
  • 1702910 Tanya, David, Rama 1881546 Eurie, Rama
    3 KB (382 words) - 03:08, 2 April 2009
  • Seth Mary Amelia Chris Ben Rama
    792 bytes (107 words) - 09:50, 4 March 2008
  • Rama Balakrishnan (SGD) and Shengqiang Shu (Berkeley) * Rama Balakrishnan (SGD)
    4 KB (651 words) - 05:58, 13 December 2018
  • Rama<br>
    2 KB (258 words) - 10:18, 30 June 2014
  • <span style="font-weight: bold; color: blue">rama</span>: Karen is out at a meeting. I agree we should wait. <span style="font-weight: bold; color: blue">jrichter</span>: How's about... Rama or Harold? Can you do it? (If you volunteer now, you're off the hook the ne
    31 KB (4,894 words) - 02:20, 13 July 2006
  • <span style="font-weight: bold; color: blue">rama</span>: I second that idea. <span style="font-weight: bold; color: blue">rama</span>: Karen- Is Mike going to test this today?
    13 KB (2,042 words) - 02:24, 13 July 2006
  • <span style="font-weight: bold; color: blue">rama</span>: What was it? I have the same problem. <span style="font-weight: bold; color: blue">jrichter</span>: Rama - The first thing to do is make sure that the reasoner is turned off. That'
    34 KB (5,610 words) - 02:24, 13 July 2006
  • <span style="font-weight: bold; color: blue">rama</span>: yeap, sounds good! <span style="font-weight: bold; color: blue">rama</span>: in beta20, i see the is_a icons but I don't see the part_of icons.
    32 KB (5,194 words) - 02:26, 13 July 2006
  • <span style="font-weight: bold; color: blue">rama</span>: Sure <span style="font-weight: bold; color: blue">midori</span>: Rama wanted to "save all the 'is_a' children (and is_a grand children and is_a g
    39 KB (6,163 words) - 02:27, 13 July 2006
  • ...elt they couldn't keep up. Now, none of us edit at all. After the webinar, Rama and I now feel almost up to speed
    25 KB (4,125 words) - 02:30, 13 July 2006
  • <span style="font-weight: bold; color: blue">rama</span>: Hi All, Welcome to our first IRC Chat <span style="font-weight: bold; color: blue">rama</span>: We are waiting for Pascale and Val
    44 KB (7,096 words) - 02:32, 3 August 2006
  • *Rama Balakrishnan (SGD)
    4 KB (658 words) - 06:57, 8 April 2014
  • outreach. Karen, Eurie, and Rama were the main organisers.<br>
    7 KB (1,287 words) - 05:15, 15 April 2019
  • *[[AmiGO help Term Search Results|Term Search Results]] : Rama
    2 KB (283 words) - 05:05, 14 December 2006
  • -Rama
    3 KB (508 words) - 06:34, 9 April 2019
  • GO effort organized by Rama Balakrishnan.<br> Teaching by Rama Balakrishnan, Trudy Torto-Alalibo, Fiona McCarthy,
    5 KB (743 words) - 05:16, 15 April 2019
  • * Rama: ''Its difficult to find time.'' * Rama: Suzi has been talking to JGI, they use the InterPro2GO mapping but don't c
    6 KB (1,047 words) - 13:24, 9 April 2014
  • == Should GO be represented at JGI users meeting? Rama has volunteered. == MA: Left up to Mike and Rama. If Rama goes she should be briefed. Jane to send an email to JGI as follow up.
    6 KB (976 words) - 08:50, 30 June 2014
  • * PAG meeting (Organized by Rama Balakrishnan, See wiki for full details.) * For SGD Karen is now on Ontology Development and Rama is on Outreach.
    4 KB (686 words) - 08:54, 30 June 2014
  • <span style="font-weight: bold; color: blue">rama</span>: nope <span style="font-weight: bold; color: blue">rama</span>: How about searching by kingdoms?
    20 KB (3,235 words) - 09:58, 13 February 2007
  • :Rama has suggested two - one at JGI, and the next rice meeting in Japan
    12 KB (1,933 words) - 08:31, 30 June 2014
  • Rama Balakrishnan has sent emails to users she met at the PAG meeting inviting t
    4 KB (583 words) - 05:12, 15 April 2019
  • == Rama Balakrishnan for SGD==
    7 KB (1,106 words) - 07:55, 3 March 2009
  • - Organized full-day workshop on GO, with Harold Drabkin, Rama 1232708 - Rama Balakrishnan, Kimberly Van Auken, Val Wood
    3 KB (513 words) - 08:22, 6 May 2014
  • 1490810 - Rama Balakrishnan
    5 KB (629 words) - 07:43, 20 August 2009
  • Planning for PAG outreach (Jen, with Rama, Trudy, Michelle, Fiona 1532264 - Rama Balakrishnan, Val Wood
    5 KB (770 words) - 14:38, 14 July 2014
  • 1587325 - Emily, David, Rama
    4 KB (521 words) - 02:50, 2 April 2009
  • 1592307 - Rama 1598086 - Rama
    4 KB (506 words) - 02:51, 2 April 2009
  • 1589414 - Harold, Rama
    4 KB (522 words) - 02:51, 2 April 2009
  • 1654525 - Harold, Rama 1646580 - Rama
    5 KB (722 words) - 02:52, 2 April 2009
  • Attending: Jen, Evelyn, Rama, Michelle, Fiona, Pascale. Rama: Uses email as a daily prioritization.
    5 KB (906 words) - 13:26, 9 April 2014
  • Present- Rama, JenC, Evelyn, Fiona, Pascale, Michelle<br> Rama: What is the format of this meeting? What is the role of GO?<br>
    3 KB (616 words) - 13:25, 9 April 2014
  • the transport interest group, Maria, Rama, and David for further comments? ...ussed the specific case of ?chaperone activity?, which has been obsoleted. Rama explained that the word ?chaperone? is used to mean three separate activiti
    15 KB (2,404 words) - 06:22, 16 December 2008
  • 1585196 - Houg, Rama 1652533 - Rama, John G
    6 KB (887 words) - 02:53, 2 April 2009
  • Rama Balakrishnan, Evelyn Camon, Jennifer Clark, Harold Drabkin*, Michelle Gwinn
    3 KB (556 words) - 13:23, 9 April 2014
  • <p class="p2"><span class="s6"><a href="irc://irc.macnn.com/rama,isuser"><b>rama: </b></a></span>I tested it briefly and nothing is broken as far as I can t <p class="p6"><span class="s6"><a href="irc://irc.macnn.com/rama,isuser"><b>rama: </b></a></span><a href="http://toy.lbl.gov:9002/cgi-bin/amigo/go.cgi"><spa
    25 KB (4,873 words) - 10:48, 9 April 2014
  • 1695255 - Rama
    4 KB (633 words) - 02:53, 2 April 2009
  • Maria Costanzo, Karen Christie, and Rama Balakrishnan (SGD staff)<br>
    1 KB (185 words) - 05:13, 15 April 2019
  • ...plex? How long should the interaction last for it to be called a complex? (Rama) ## Boundary between ISS & RCA and scope of RCA evidence code (Michelle and Rama (filling in for KarenC); see [http://genetics.stanford.edu/~kchris/go/evCod
    11 KB (1,617 words) - 16:26, 8 April 2014
  • rama: cool. thanks Ben rama: I agree. It is clear to me.
    7 KB (1,239 words) - 10:50, 9 April 2014
  • gwg: hi Ben, hi Rama rama: hello
    9 KB (1,683 words) - 10:48, 9 April 2014
  • Present: Rama, Michelle, Pascale, Harold ...d look for to start making GO annotations. We discussed the flowchart that Rama had sent to the group sometime back (also posted on the wiki).
    1 KB (212 words) - 13:25, 9 April 2014
  • ACTION: Eurie will talk to Rama
    4 KB (716 words) - 08:48, 30 June 2014
  • * Rama will look after outreach group while Jen is away
    2 KB (302 words) - 09:01, 30 June 2014
  • Participants: Fiona McCarthy, Michelle Gwinn, Jennifer Deegan, Rama Balakrishnan, Pascale Gaudet, did I miss anyone?
    2 KB (374 words) - 13:24, 9 April 2014
  • * Rama mentioned international meeting on rice genomics; see http://www.isrfg2007.
    6 KB (1,022 words) - 08:42, 30 June 2014
  • **Rama: EBI SRS
    680 bytes (99 words) - 14:44, 8 April 2014
  • rama has joined the channel rama: gwg- please translate
    12 KB (2,201 words) - 14:46, 8 April 2014
  • rama has joined the channel gwg: Hi Rama!
    11 KB (2,178 words) - 10:49, 9 April 2014
  • *SRS: Rama
    350 bytes (53 words) - 14:44, 8 April 2014
  • ...r><font color="#9440B1"><font size="2">(09:56:58 AM) </font><font size="3">rama:</font></font><font size="3"> thanks</font><br><font size="2"><font color="
    41 KB (6,553 words) - 10:49, 9 April 2014
  • 1753808 - Karen, Rama 1754690 - Val, Rama
    4 KB (507 words) - 03:05, 2 April 2009
  • rama: Aren't we doing what Princeton does? Provide all GA files in a pull down? rama: I think Matts request should be an enhancement- shd add to SF
    10 KB (1,833 words) - 10:50, 9 April 2014
  • Rama<br>
    25 KB (3,637 words) - 14:48, 23 April 2014
  • 1768428 Rama, Val 1771167 Rama
    3 KB (444 words) - 03:05, 2 April 2009
  • There hasn't been any discussion of the papers Rama suggested for the RCA discussion, but if you read them you'll notice that t
    17 KB (3,069 words) - 01:51, 16 April 2019
  • '''2001''' Rama Balakrishnan SGD, Michelle Gwinn Giglio TIGR, Harold Drabkin MGI
    36 KB (5,808 words) - 06:12, 15 April 2019
  • Pascale G, Rama B: New groups might not be able to handle this. How many new groups are req Rama B: these is a draft web page ready, with the majority of text and examples
    25 KB (4,182 words) - 06:12, 15 April 2019
  • '''2001''' Rama SGD, Michelle TIGR, Harold Drabkin MGI
    32 KB (5,124 words) - 06:12, 15 April 2019
  • ...oday. Create documentation for curators and users (more succinct version) (Rama and the Evidence Code committee) ...ation in only one gene can only be IMP (protein localization IGI example) (Rama)
    4 KB (585 words) - 06:12, 15 April 2019
  • ...web presence group in the advocacy monthly reports. She will contact Ben, Rama and Amelia to ask them to contribute information to the report. ...web presence group in the advocacy monthly reports. She will contact Ben, Rama and Amelia to ask them to contribute information to the report. <br>
    11 KB (1,951 words) - 08:46, 30 June 2014
  • ..."#AB5871">(08:38:09 AM) </font></font><font color="#AB5871"><font size="3">rama:</font></font><font size="3"> no worries</font><br> ..."#AB5871">(08:39:23 AM) </font></font><font color="#AB5871"><font size="3">rama:</font></font><font size="3"> we are waiting for?</font><br>
    26 KB (4,130 words) - 18:19, 8 November 2007
  • # A summary email of of the chat, combined with Ben and Rama's comments, will be sent out for further discussion
    546 bytes (81 words) - 18:18, 8 November 2007
  • ...web presence group in the advocacy monthly reports. She will contact Ben, Rama and Amelia to ask them to contribute information to the report. [not yet do
    5 KB (738 words) - 09:01, 30 June 2014
  • 1669585 Rama, Rob, Val 1237306 Rama, Rob, Val, Simon
    3 KB (447 words) - 03:06, 2 April 2009
  • Seth, Amelia, Rama * Rama said just send mail to group
    756 bytes (121 words) - 19:22, 8 November 2007
  • Rama, Eurie, Mary, Amelia, Seth, Chris
    1 KB (167 words) - 19:22, 8 November 2007
  • Chair: Rama<br> *About meeting Chairs- No body in the group (other than Ben and Rama) was aware of the reverse order of Chairs for Hub and WG meetings. We decid
    4 KB (717 words) - 19:23, 8 November 2007
  • ...that people remember these meetings and call/logon etc without reminders (Rama)
    1 KB (184 words) - 19:24, 8 November 2007
  • ...web presence group in the advocacy monthly reports. She will contact Ben, Rama and Amelia to ask them to contribute information to the report. [not yet do
    3 KB (527 words) - 08:43, 30 June 2014
  • ** Search: Rama/Eurie (Eurie from email)
    1 KB (158 words) - 11:31, 28 November 2007
  • how about rama? is she still away? <val> That leaves search for rama
    8 KB (1,372 words) - 11:32, 28 November 2007
  • 1825979 Val, Rama
    3 KB (427 words) - 03:06, 2 April 2009
  • Seth, Amelia, Rama, Ben, Mary
    606 bytes (82 words) - 17:54, 5 December 2007
  • Seth, Amelia, Rama, Ben, Chris, Suzi
    730 bytes (105 words) - 09:54, 18 December 2007
  • ...web presence group in the advocacy monthly reports. She will contact Ben, Rama and Amelia to ask them to contribute information to the report. Amelia is s
    5 KB (915 words) - 08:37, 30 June 2014
  • 1849534 Donghui, Rama, Karen C
    3 KB (390 words) - 03:06, 2 April 2009
  • Rama ...to proceed with planning. Fiona is going to have a number of meetings with Rama and Harold. Jen also will attend as required. <br>
    4 KB (691 words) - 06:10, 15 April 2019
  • <font size="2">(08:36:46 AM) </font><b><font size="3">rama [<i>rama@c-24-7-123-136.hsd1.ca.comcast.net</i>] entered the room.</font></b><br> ..."#AB5871">(08:36:57 AM) </font></font><font color="#AB5871"><font size="3">rama:</font></font><font size="3"> Hi, sorry I am late</font><br>
    38 KB (5,929 words) - 10:57, 24 January 2008
  • Seth, Ben, Rama
    552 bytes (70 words) - 17:06, 18 March 2008
  • ...ont><font color="#3F1AB3"><font size="3">ben:</font></font><font size="3"> Rama is out</font><br> ...(08:47:07 AM) </font><font size="3">gwg:</font></font><font size="3"> only Rama replied, which was very solicitous of her...</font><br>
    46 KB (7,168 words) - 14:03, 16 July 2014
  • 1909714 Rama 1911964 Rama, Val
    3 KB (411 words) - 03:08, 2 April 2009
  • Rama, Chris, Ben, Jane, Seth, Mary
    1 KB (193 words) - 08:18, 15 April 2008
  • Ben, Seth, Amelia, Rama, Chris
    708 bytes (100 words) - 09:24, 7 May 2008
  • Mary, Seth, Amelia, Rama, Ben
    1 KB (183 words) - 08:14, 16 September 2008
  • ...tation – abbreviated version on web pages and more detailed on GOC Wiki (Rama) 13. Sue, Michelle, Rama put evidence code proposal in the context of what we discussed today
    31 KB (4,938 words) - 06:06, 15 April 2019
  • Seth, Amelia, Rama, Ben, Jane * What is release schedule for current bugfix (rama)
    2 KB (345 words) - 17:08, 20 May 2008
  • Chris, Jane, Amelia, Ben, Rama, Mary
    670 bytes (100 words) - 08:38, 3 June 2008
  • 1969138 Rama, Julie
    3 KB (414 words) - 03:07, 2 April 2009
  • Seth, Amelia, Mary, Chris, Rama, Ben * rama to do a final round for this bug release
    823 bytes (126 words) - 14:13, 17 June 2008
  • * rama to do a final round for this bug release [DONE]
    905 bytes (136 words) - 07:59, 1 July 2008
  • 1508524 Rama 1536003 Rama, Val
    3 KB (430 words) - 03:07, 2 April 2009
  • |Rama Balakrishnan
    9 KB (1,291 words) - 06:06, 15 April 2019
  • 1729553 Rama 1778552 Val, Rama, Karen C
    3 KB (366 words) - 03:10, 2 April 2009
  • rama has joined the channel jenclark: rama is your microphone muted?
    96 KB (16,723 words) - 14:08, 30 June 2014
  • rama has joined the channel rama: John-Boy or Girl?
    37 KB (6,547 words) - 14:08, 30 June 2014
  • rama has joined the channel rama has quit the server saying: Quit: rama
    22 KB (3,784 words) - 14:09, 30 June 2014
  • Amelia, Seth, Rama, Mary
    1 KB (225 words) - 09:06, 5 August 2008
  • I'm not sure my stand it, likely Rama, will get involved with testing, but since SGD is the production environmen OK, sounds good John, but I think Rama will be able to sit in for at least the business part to keep in touch with
    27 KB (3,902 words) - 06:30, 1 July 2014
  • *Should we send people to PAG again this year? If so, then shall we ask Rama again, as she has been doing it for the last few years and has done well. F ...he is happy to take the lead if David helps. She is also going to write to Rama to ask if she will be there this year.
    2 KB (400 words) - 08:30, 30 June 2014
  • Mary, Seth, Amelia, Ben, Rama, Jane *** Rama volunteered
    1 KB (187 words) - 08:04, 19 August 2008
  • #Rama Balakrishnan, Ph.D., Senior Scientific Curator, Saccharomyces Genome Databa
    12 KB (1,521 words) - 05:06, 12 April 2019
  • ...he is happy to take the lead if David helps. She is also going to write to Rama to ask if she will be there this year.
    4 KB (756 words) - 12:02, 7 April 2014
  • (08:43:41 AM) sjcarbon: I guess Rama will be here soon... (08:47:25 AM) rama [rama@c-24-7-118-198.hsd1.ca.comcast.net] entered the room.
    20 KB (3,121 words) - 14:04, 16 July 2014
  • 981451 David, Michelle, Rama 2034849 Rama, John Garavelli
    3 KB (421 words) - 03:11, 2 April 2009
  • Pascale, Ben, Chris, Amelia, Rama, Seth
    854 bytes (126 words) - 11:31, 24 November 2008
  • <font size="2">(08:32:35 AM) </font><b><font size="3">rama [<i>rama@c-24-7-118-198.hsd1.ca.comcast.net</i>] entered the room.</font></b><br> ..."#AB5871">(08:33:31 AM) </font></font><font color="#AB5871"><font size="3">rama:</font></font><font size="3"> hello</font><br>
    36 KB (5,658 words) - 14:05, 16 July 2014
  • 2047476 Rama 2100734 Rama
    4 KB (451 words) - 03:11, 2 April 2009
  • Seth, Mary, Ben, Rama, Chris, Amelia
    1 KB (203 words) - 13:35, 8 October 2008
  • Rama Balakrishnan, Gail Binkley, Karen Christie, Maria Costanzo, Selina Dwight,
    5 KB (696 words) - 07:57, 20 August 2009
  • Seth, Suzi, Siddartha, Pascale, Edith, Michael (Princeton), Amelia, Chris, Rama, ...
    2 KB (253 words) - 09:53, 4 November 2008
  • Rama, Dianna, Rachael, Prudence, Li, Midori, Doug, Becky, Chris, Antonia, Ruth, '''1. GO Mine presentation (Rama)'''
    2 KB (250 words) - 12:28, 9 April 2014
  • edith, michael, kimberly, seth, amelia, pascale, rama, mary
    2 KB (274 words) - 10:46, 18 November 2008
  • Michael, Pascale, Rama, Siddartha, Chris, Seth
    802 bytes (121 words) - 09:45, 25 November 2008
  • <rama> no problem <rama> yes
    10 KB (1,749 words) - 14:05, 16 July 2014
  • 2100763 Karen C, Rama, Val
    3 KB (415 words) - 03:12, 2 April 2009
  • Ben, Seth, Chris, Mary, Rama
    1 KB (189 words) - 09:29, 2 December 2008
  • 2435061 Val, Rama 2435063 Val, Rama
    3 KB (403 words) - 03:11, 2 April 2009
  • Rama Balakrishnan, Gail Binkley, Karen Christie, Maria Costanzo, Selina Dwight,
    5 KB (703 words) - 07:56, 20 August 2009
  • | Rama Balakrishnan | rama@genome.stanford.edu*
    12 KB (1,878 words) - 07:51, 12 April 2019
  • ** Rama: what would the user see? ** Tanya: To answer Rama and Ranjana: people need to use information from the graph anyway
    29 KB (4,509 words) - 06:06, 15 April 2019
  • Seth, Petra, Stacia, Amelia, Chris, Rama, Jane * Rama to send list of WPWGers to Seth
    1 KB (160 words) - 17:16, 27 January 2009
  • ...al;'><font size="2">(08:35:13 AM) </font></span><b><font size="3">rama [<i>rama@c-98-207-117-165.hsd1.ca.comcast.net</i>] entered the room.</font></b><br> ...nt></span><font size="3"><span style='font-weight: normal;color: #ab5871;'>rama: </span>hi there</font><br>
    66 KB (10,007 words) - 14:05, 16 July 2014
  • 2503103 Rama 2507331 Eurie, Rama, Val
    4 KB (473 words) - 03:11, 2 April 2009
  • 2012346 Julie, Rama 2597089 Julie, Rama
    4 KB (470 words) - 03:11, 2 April 2009
  • Seth, Pascale, Amelia, Rama, Chris, Eurie * get rama's rg example queries onto GOOSE example wiki (seth)
    629 bytes (84 words) - 09:50, 24 March 2009
  • ...al;'><font size="2">(08:30:45 AM) </font></span><b><font size="3">rama [<i>rama@cider.Stanford.EDU</i>] entered the room.</font></b><br> ...nt></span><font size="3"><span style='font-weight: normal;color: #ab5871;'>rama: </span>hello</font><br>
    37 KB (5,630 words) - 14:06, 16 July 2014
  • Jane, Seth, Pascale, Amelia, Rama * take a quick look at GOOSE on new site (Rama)
    1 KB (220 words) - 08:13, 28 April 2009
  • ...al;'><font size="2">(08:41:12 AM) </font></span><b><font size="3">rama [<i>rama@cider.Stanford.EDU</i>] entered the room.</font></b><br> ...nt></span><font size="3"><span style='font-weight: normal;color: #ab5871;'>rama: </span>hi there</font><br>
    26 KB (4,000 words) - 14:06, 16 July 2014
  • Rama, Seth, Amelia, Ben, Jane
    3 KB (502 words) - 09:36, 19 May 2009
  • Rama, Seth. * get rama's rg example queries onto GOOSE example wiki (seth)
    810 bytes (112 words) - 07:49, 26 May 2009
  • Mary, Rama, Ben, Seth, Amelia * get rama's rg example queries onto GOOSE example wiki (seth)
    1 KB (151 words) - 08:35, 2 June 2009
  • ...nt></span><font size="3"><span style='font-weight: normal;color: #ab5871;'>rama: </span>seth?</font><br> ...nt></span><font size="3"><span style='font-weight: normal;color: #ab5871;'>rama: </span>okay. sounds good. bye</font><br>
    1 KB (218 words) - 14:06, 16 July 2014
  • Present: Pascale, David, Judy, Emily, Paul S, Rama, Mike C, Chris ==Paper on GAF (Rama)==
    2 KB (382 words) - 11:30, 27 June 2014
  • * get rama's rg example queries onto GOOSE example wiki (seth)
    674 bytes (90 words) - 15:01, 22 June 2009
  • Seth, Amelia, Rama, Ben * Gather data files for automated testing (Seth and Rama)
    948 bytes (138 words) - 08:55, 25 August 2009
  • * get rama's rg example queries onto GOOSE example wiki (seth)
    720 bytes (100 words) - 09:56, 24 August 2009
  • ...al;'><font size="2">(08:33:07 AM) </font></span><b><font size="3">rama [<i>rama@cider.Stanford.EDU</i>] entered the room.</font></b><br> ...nt></span><font size="3"><span style='font-weight: normal;color: #ab5871;'>rama: </span>Good morning</font><br>
    13 KB (1,991 words) - 14:07, 16 July 2014
  • Chris, Jane, Ben, Amelia, Seth, Rama, Edith ** Big testing push: amelia, jane, rama
    2 KB (243 words) - 08:11, 1 September 2009
  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Karen Christie, Maria Costan
    4 KB (612 words) - 15:34, 6 March 2020
  • *(Rama)We need an annotation camp. It’s been several years.
    41 KB (6,404 words) - 06:13, 15 April 2019
  • Ben, Jane, Rama, Amelia, Mary, Seth
    1 KB (215 words) - 10:26, 2 February 2010
  • Rama: perhaps at end of year, we could take a break to focus on annotation and e ===Annotation 1: Binding (Rama, Emily) ===
    54 KB (8,575 words) - 07:51, 12 April 2019
  • Ben, Kalpana, Seth, Rama, Jane, Chris, Amelia
    1 KB (150 words) - 14:52, 21 December 2009
  • * rama has joined the room rama: Hello,
    9 KB (1,692 words) - 14:07, 16 July 2014
  • Seth, Amelia, Rama * Rama's edits to 1.7 announcement
    1 KB (213 words) - 10:59, 1 December 2009
  • ...come up with a way to represent the chaing of evidence. '''Action item''': Rama et al will form a working group on chain of evidence/LEGO and come up with
    3 KB (448 words) - 08:20, 8 April 2014
  • * Rama and Eurie on SGD's practice-
    7 KB (1,007 words) - 07:47, 12 April 2019
  • * Chris, Harold, Doug, Rama, Kimberly, Mary, Ruth, Pascale, Jim, Doug, Fiona, Lakshmi, Val, Yasmin, Emi ''Rama:'' Perhaps GO is not the best resource to capture such detail, curators nee
    17 KB (2,801 words) - 09:51, 4 June 2014
  • From Rama Balakrishnan and Julie Park:
    3 KB (441 words) - 14:38, 15 July 2014
  • Rama Balakrishnan*,
    4 KB (526 words) - 15:34, 6 March 2020
  • | Rama Balakrishnan
    9 KB (1,296 words) - 07:48, 12 April 2019
  • *Annotation & Curation (Rama Balakrishnan, Emily Dimmer)
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  • * SGD: Julie, Stacia, Rama Rama: technical issues vs are we agreed that we want to create a separate GO_Ref
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  • ben: rama suggested moving the golite (amigo) db load back a day or two so that it wi
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  • == Things on Rama's list ==
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  • * SGD: Rama, Julie
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  • Participants: David, Kara, Pascale, Judy, Rama, Midori, Jane, Emily
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  • # [Rama] Write to Chris, David, Tanya about Inter-ontology links - frequency of upd # [Rama] Organize annotation managers wiki page using what is currently in the Refe
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  • Seth, Ben, Rama
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  • *** GAF inference and Evidence codes for automated inference (5-10 - Chris, Rama) *** GAF2 update (5-10) CJM/Rama
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  • | Rama '''Chair: Rama Balakrishnan'''
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  • == InterOntology links / annotations - Rama, Tanya, David email==
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  • Mary, Rama, Chris, Seth, Amelia * rama to try another icon mockup
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  • ...d contributing resources. Rama Balakrishnan (15 min) Presentation: [[File: Rama-intro-to-annotation.pdf]] *'''Chairs: Rama Balakrishnan and TBA from Swiss-Prot'''
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  • ...er, Pascale Gaudet, Rachael Huntley, Yasmin Alam-Faruque, Varsha Khodiyar, Rama Balakrishnan, Ruth Lovering, Kimberly Van Auken (minutes) ''Rama:'' Is receptor internalization a consequence of the kinase activity?
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  • Present: Ruth Lovering (Chair), Rama, Jodi, Jim Hu, Li, Becky Rama: tool being developed to create these reciprocal annotations. This was a so
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  • | Rama
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  • # (Rama:) Interpretation of author statements: Authors very often use the word comp Peter, Judy, Suzi, Rama, Pascale, Emily, Harold, Diana, Serenella, Cecilia, Chris.
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  • Participants: Rama, Kara, Pascale, Suzi, Judy, Midori, Emily, Chris Rama - communicating with Vinoid from the M.tuberculosis annotation jamboree eff
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  • Seth, Sven, Pascale, Amelia, Ben, Rama, Chris
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  • - rama has joined the room rama: hi
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  • Minutes: Rama Present: Rama, Emily, Jane, MikeC, David, Judy, Suzi, Pascale<br>
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  • #* Rama: perhaps at end of year, we could take a break to focus on annotation and e ===Annotation 1: Binding (Rama, Emily) ===
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  • - Association file Readme updates (Rama)- oops, i was thinking of a SOP document that we put together some time bac *Rama- High-throughput working group
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  • ...t "ATP hydrolysis" is an exact synonym. Pascale has sent this question to Rama and Emily.
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  • Participants: Kara, Jane, Rama, Chris, Suzi, Mike, Pascale Agenda: Rama
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  • Action: Emily to send Rama email addresses for working groups ...amp and ECO discussion. Move to issues page, to be resolved later. Action: Rama.
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  • * rama to try another icon mockup
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  • * pasc: Rama said she can't make it
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  • * Rama Balakrishnan
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  • ...</span>@<span class="place">genome.stanford.edu</span> (<span class="name">Rama Balakrishnan</span>)</span> (SGD) ...</span>@<span class="place">genome.stanford.edu</span> (<span class="name">Rama Balakrishnan</span>)</span> (SGD)
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  • ** Rama: Should curators keep on requested GO Complexes terms? Judy, yes, we need t
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  • * SGD: Rama, Julie # HTP: Rama Balakrishnan (Wiki page: [[2010_GO_camp_Annotation_of_HTP_data]])
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  • Present: Varsha, Becky, Pascale, Karen, Yasmin, Ruth, Li, Rama, Michele G. * Rama, Karen and Li would NOT use response to in this situation.
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  • * Discuss Roadmap for Annotation Advocacy group (rama) | ...ce code ECO proposal- who should take the initiative to move this forward (Rama)
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  • Rama: both running and generating scripts. Rama: email OEWG
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  • ...annotation sessions (Yasmin has agreed for 'downstream effects'). (Action: Rama) - Rama: sent mail to Chris and Michelle (no response yet)
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  • * SGD: Rama, Julie # HTP: Rama Balakrishnan (Wiki page: [[2010_GO_camp_Annotation_of_HTP_data]])
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  • Present: Rachael, Rama, Emily - Rama: perhaps on the main horizaontal list on the GOC pages - instead of documen
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  • Present: David, Judy, Suzi, Rama, Pascale, Emily '''ACTION:''' Rama to add this to the AmiGO working group agenda to discuss further.
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  • *** Rama's list * rama to try another icon mockup
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  • Ben, Seth, Rama, Amelia ** Largely unknown, but Rama will be available
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  • - ACTION for Rama. GO Camp: Need to collect all talks and summary slides on wiki page and put ...Proposal to close all mailing lists and have one annotation mailing list. Rama to send email to Manager's list to propose merging certain mailing lists. S
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  • - rama has joined the room rama: morning
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  • '''ACTION:''' Rama to add this to the AmiGO working group agenda to discuss further. Rama and Pascale
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  • ...QCs for filtering script, can go in Mike's script, send email to GO list. Rama to document soft QC checks from GO camp. Rama to send mail to Mike about email lists. Make new list GO Discussions or use
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  • * 1:00-2:30: [[Annotation Advocacy and Coordination|Annotation]] Report (Rama & Rachael)- [[File: BHB2010.pdf]] *#* Annotation & reference genome groups communication (Pascale and Rama)
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  • Present: Suzi, Judy, Pascale, Rama, Rachel, David
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  • Seth, Ben, Chris, Rama. * Rama to see who is available for testing.
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  • - rama has joined the room rama: hello
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  • |Rama Balakrishnan
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  • * SGD: Rama
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  • - Write to all mailing lists to announce merge. Rama to check with Mike whether we should sign up or be automatically signed up. - Rama will send out email
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  • ...annotation_related mailing list was agreed upon at the last Managers call. Rama will make an announcement about the merge and the merge will potentially ha *Rama is looking into reorganizing the Annotation_documentation section on the GO
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  • ...) [Working group to be established; including Harold and Amelia]. Manager: Rama and Emily ...working group to investigate revamp of evidence codes. Manager: Emily and Rama
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  • Present: Judy, Kara, Pascale, Rachael, Rama, Chris ...We will ask MODs to prepare one and get them on the wiki before Dec 2010. Rama will create a page for GRANT 2010 and add links.
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  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Karen Christie, Maria Costan
    4 KB (574 words) - 15:34, 6 March 2020
  • ...) [Working group to be established; including Harold and Amelia]. Manager: Rama and Emily. ...working group to investigate revamp of evidence codes. Manager: Emily and Rama
    2 KB (357 words) - 12:12, 9 April 2014
  • ...e GOA database. The annotations were reviewed by Rachael Huntley (GOA) and Rama Balakrishnan (SGD) and were deemed to be of high-quality. Almost 5800 annot
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  • Rama about these and we have both spot-checked quite a few of the in column 16. Rama and I feel that these mistakes could be corrected
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  • Rama
    2 KB (249 words) - 07:19, 16 January 2018
  • ...e approx. 6000 annotations of which ~3000 are from high-throughput papers. Rama and Rachael checked many of the annotations which were of high-quality. Aft
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  • **Files are in CVS now. Rama will follow up with Chris to see if an email can be fired when new files ge * ECO proposal -sent mail to Chris and Michelle (no response yet)- Rama will follow up with Chris etc. Possibly wrap into Chain of evidence proposa
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  • ...ing group on evidence codes: proof of principle for chain of evidence: WG: Rama (will follow up), Paul, Alex, Suzi, Peter D? other curators? (including Le * We had a phone call yesterday (Pascale, Kara, Mike L, Paul, Mike C, Rama) ; see notes [[21_SEPT_2010_RefGen_Priorities_Discussion]]
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  • (Rama) ...An automated script tests a lot of things, when moved to Stanford servers Rama tests again then sends out email to ask for more testing. Suzi recommends t
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  • * Pascale started to train Rama to use PAINT.
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  • Pascale, Kara, Mike L, Paul T, Rama
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  • ====Annotation Advocacy Group Report (Rama)==== Rama went through the recent accomplishments of the annotation advocacy group. O
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  • ...base. The annotations were reviewed by Rachael Huntley (UniProtKB-GOA) and Rama Balakrishnan (SGD) and were deemed to be of high-quality. The annotations w * Together with Rama Balakrishnan from SGD, Emily Dimmer is a manager for the GO Consortium's An
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  • ...on yeast transcription and send their annotations to Rama by 5th November. Rama will collate the annotations and a call-based discussion will happen on 8th
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  • Rama waiting to hear from Mike. Rama and Pascale to send comments to Rachael.
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  • Kara Dolinski, Pascale Gaudet, Rachel, Jane, David Hill, Rama, Chris, Mike C, Judy, Suzi, Paul Sternberg, Paul Thomas *Updating annotation documentation: Rama. Talking to Amelia about final touches (tabs on pages); text is good to go
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  • Present: SGD- Rama, Karen, Julie, Jodi, Ruth, Rachael, Yasmin, Kimberly, Stan, Tim, Tom, Shur- ...y of the month). If any of you have issues with this schedule please email Rama and Rachael.<br>
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  • ...MF-BP inferences are on the FTP site? Are there any technical questions? -Rama
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  • * SGD: Rama Rama, Li, Dmitry, and maybe others will start doing tree annotations. In Decembe
    2 KB (389 words) - 07:15, 16 January 2018
  • * Rama and Karen had a phone conference call with Michelle and Marcus about ECO. W ...currently listed as a soft QC. They are of the kind 'resolution deferred'- Rama will fix the specs page to reflect this difference.
    10 KB (2,007 words) - 11:09, 27 June 2014
  • ...e GOA database. The annotations were reviewed by Rachael Huntley (GOA) and Rama Balakrishnan (SGD) and were deemed to be of high-quality. Almost 5800 annot
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  • ...to Mike Livstone, 4 other curators have been trained to do PAINT curation: Rama Balakrishnan, Varsha Khodiyar, and (Nov 19) Li Ni and Dmitry Sitnikov
    10 KB (1,317 words) - 06:39, 16 January 2018
  • Jane, Emily, Rama, David, Mike, Chris, Paul T and Paul S
    2 KB (431 words) - 11:13, 27 June 2014
  • Rama Balakrishnan,
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  • ...the [http://www.geneontology.org/GO.annotation_qc.shtml RuleEngine page] (Rama, Amelia), GO taxon contraints reviewed for manual annotations in the GOC, f ...el organisation of pages (Rama, Emily, Rachael, Harold?) and page display (Rama and Amelia)
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  • * Rama
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  • Emily, Pascale, Rama, Chris, Paul S, Suzi, Judy, David, Paul T * Rama? Make the meeting rota for 2011
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  • - Rama to send her month's of stats - and Emily to generate first draft web page f
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  • Present: Pascale, Rama, Judy, Paul S, David, Kara, Suzi, Paul T, Emily
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  • David, Rachael, Paul T., Judy, Kimberly, Rama, Chris, Huaiyu, Paul S., Pascale. # CANTO deployment (Chris, Seth, Kim, Rama)
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  • * InterPro-source advocated for InterPro2GO etc. Emily to send Rama a draft
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  • ==Paper on GAF (Rama)==
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  • ** not discussed today but a very nice example from Rama - sequence is extremely conserved, annotation to AN0 can be done even thoug
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  • ** AI: Karen will check with Rama about whether the AmiGO hub meetings are still active, then we can make a d
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  • * Rama: Document cron job for trees * Rama: Everyone needs to communicate to the software team to upload the MF-BP inf
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  • ==Paper on GAF (Rama)==
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  • (Rama, Emily, Pascale) [http://wiki.geneontology.org/index.php/Annotation_Advocac ===10:15 Community resources and Dissemination (Emily & Rama)===
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  • * Rama SGD ...upload the MF-BP inferences on the FTP site (ADD LINK TO DOCUMENTATION). (Rama, everyone) On hold. Chris wants people to make the annotations manually on
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  • ...anization of curator guidelines in the GO Consortium annotation web pages (Rama)- http://www.geneontology.org/newIndex.shtml
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  • Attending: Rama, Pascale, Suzi, Judy, David, Emily, PaulT<br> Minutes by Rama
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  • | Rama Balakrishnan
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  • #1 Literature annotation; (Judy and Rama) #6 Dissemination and outreach (Mike and Rama, Emily, and perhaps Seth to stand in for Chris and really being the front-o
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  • * Rama SGD #Move PAINT evidence codes to official documentation (Done, Rama)
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  • *Rama Balakrishnan
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  • GO managers: Rama Balakrishnan and Emily Dimmer, who support the work carried out by the GO C
    2 KB (357 words) - 11:50, 9 April 2014
  • * '''Annotation''': Contact Rama and Emily if you can help organizing and editing the annotation pages on th Responsible: Rama and Emily will moderate, include in annotation calls ONGOING
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  • Meeting canceled since only Rama and David were the only ones attending.
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  • Rama SGD; *Rama asked about the proposed structure - is signal transduction in the same bra
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  • * Rama SGD
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  • |Rama Balakrishnan
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  • Present: Rama, Julie, Jodi, Karen, Rob Nash, Dianna (SGD)<br>
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  • * Ontology reports/email digests. Where did we get up to with this? Rama asked again this week.
    2 KB (324 words) - 07:21, 6 July 2011
  • ...l for volunteers to adopt a GO annotation guidance page (contact Emily and Rama)
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  • Present: Midori, Val, Antonia, Emily, Susan, Yasmin, Rama, Yuri, Dianna, Karen, Jodi, Judy, Li, Donghui, Kimberley, Stan, Shur-Jen, V '''Action:''' Rama and Emily to draft a GO_REF and circulate it around the GO list.
    7 KB (1,147 words) - 12:29, 9 April 2014
  • * Presentation on GOMine (Stanford group) (Rama) ...ontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap] overview (Rama)
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  • SGD: Rama, Julie, Karen, Jodi<br> ...s all set to go. Remember to make annotations to the granular annotations. Rama will add it to the GO_REF page and the Documentation page. We will also com
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  • Present: Judy, David, Jane, Rama, Pascale, Chris and Suzi<br>
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  • GO managers: Rama Balakrishnan and Emily Dimmer, who support the work carried out by the GO C
    2 KB (301 words) - 11:49, 9 April 2014
  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Karen Christie, Maria Costan
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  • Minutes: Rama, Karen ** transcription overhaul (Rama & Karen) [[Media:TxnOH-OntDev-Report.pdf]], [[Media:TxnOH-AnnotReport.pdf]]
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  • |Rama Balakrishnan
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  • Present: Petra, Pascale, Rama, Julie, Karen, Peter, Chris, Rachael, Emily, Prudence, Yasmin, Becky, Paola Rama: are the counts outlined in the document including the automatically inferr
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  • ** Rama and Emily send summary of txn and apoptosis case studies ** Paul, Emily, Harold Rama will meet to talk about what is the minimum requirement for annotations
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  • ...Ontology by Computer [[Evidence for Inferences based on Ontology links]] (Rama) SGD: Rama, Jodi<br>
    4 KB (651 words) - 12:33, 9 April 2014
  • Present: Judy, David, Rama, Emily, Paul, Suzi, MikeC
    294 bytes (42 words) - 11:29, 27 June 2014
  • ...neontology.org/index.php/Evidence_for_Inferences_based_on_Ontology_links) (Rama) SGD: Rama, Karen, Julie, Cindy, Jodi<br>
    8 KB (1,211 words) - 12:30, 9 April 2014
  • #Develop proposal for annotation process (Suzi, Harold, Rama, Emily, Kimberly, Paul) #**Prioritization, e.g. biological domain focus (Suzi, Emily, Rama)
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  • ** Anybody planning to go? (Rama)
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  • SGD: Rama and Karen
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  • SGD: Rama, Karen, Jodi<br>
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  • * drafts of new annotation pages are being (slowly) developed by Rama and Emily [http://wiki.geneontology.org/index.php/Mock-ups_of_new_GOC_Annot
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  • '''Rama:''' why would you want your work to be checked again? ====Rama's talk - transcription ontology and annotation====
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  • '''Present:''' Rama, Karen and Jodi (MGI), Stan (RGD), Li, Mary and Judy (MGI), Kimberly (WormB Rama: A number of GOC-agreed QC checks have been added to Mike's checking script
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  • There will be a demo of TAIR's resource Thursday at 10:30AM EDST. Rama and Kimberly will join the working group.
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  • ...these cellular fraction terms. We reviewed the list of TAIR annotations in Rama's spreadsheet, most of the TAIR genes that are annotated to these terms als
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  • * NIH quarterly reports required for management groups? Rama ...re_Consortium_annotation_activities Core Consortium annotation activities] Rama, Emily
    3 KB (488 words) - 11:10, 27 June 2014
  • ...neontology.org/GO.evidence.shtml#ikr IKR evidence code] has been updated (Rama) Karen, Jodi, Rama (SGD)
    6 KB (980 words) - 12:37, 9 April 2014
  • ...neontology.org/index.php/Core_Consortium_annotation_activities) (Emily and Rama)
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  • ...t from etc. I will work on interlinking and beautifying these pages later.(Rama)
    1 KB (170 words) - 10:41, 27 June 2014
  • Rama Balakrishnan
    6 KB (892 words) - 07:52, 12 April 2019
  • ...t from etc. I will work on interlinking and beautifying these pages later.(Rama)
    1 KB (208 words) - 11:32, 27 June 2014
  • * Rama, Dianna (SGD)<br>
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  • Rama, Rachael, Chris, Kimberley, David, Huaiyu, Jane, Suzi, Pascale '''ACTION: Rama''' will take a look at what needs to be done and talk to Seth
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  • Dmitri, Brenley, Suzi, Paola, Susan, Rachael, Ruth, Petra, Rama, Bob '''Action:Rama''' to put on website after Rachael has sent edits
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  • *Rama: We are aware that the UI is not friendly. SGD so far has changed the color *Rama: The software is flexible in that if we have new data (col-16 for example)
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  • ** Biological utility survey (Rama, Ranjana) [[File: GOCwebsiteCaltech12.pdf‎]] ** GOMine InterMine for GO (Mike/Rama) ([http://celis.stanford.edu:8080/gomine-dev/template.do?name=DataSouce_GOA
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  • '''Action:''' Rama to look into retiring Stanford go-help email list: 1. 'Vacation message' wh
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  • '''Action:''' Rama to look into retiring Stanford go-help email list: 1. 'Vacation message' wh Action: Rama and Mike will discuss this further
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  • * Almost done. Estimated time: end of this week. ACTION: Rama end email when done * ACTION: Rama will communicate with go-help people about updatings newsfeeds
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  • ...s are set for the Stanford PAINT workshop. December 10-13th (yes, 4 days). Rama will make a meeting logistics page (for attendees). Seth will work with Rama and Ranjana to come up with what the page should be etc. Ideally we want so
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  • ** Report feedback on issues (Rama)
    3 KB (382 words) - 06:39, 12 April 2019
  • |Rama Balakrishnan
    3 KB (418 words) - 06:40, 12 April 2019
  • ...nd managing GOhelp JIRA'''GOhelp staff, others compile gripe list, give to Rama, so we can come up with a better solution for managing emails, reports, etc # [Rama] Rama to write the announcement, waiting for more information.
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  • |Rama Balakrishnan
    7 KB (1,257 words) - 07:53, 12 April 2019
  • ...Some of the author names/affiliations were not accurate in this NAR paper. Rama will write to NAR to see if it can be fixed.
    3 KB (474 words) - 11:23, 27 June 2014
  • * Cardinality of Col-17 (Kimberley, Rama)
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  • * Judith Blake and Karen Christie are working with Rama Balakrishnan to coordinate with Astrid Laegrid of the Norwegian University
    35 KB (3,935 words) - 11:46, 4 June 2014
  • * Together with Rama Balakrishnan from SGD, Rachael Huntley is a manager for the GO Consortium's
    17 KB (2,438 words) - 01:32, 16 April 2019
  • ...nclude annotation extension information. We currently have over 30,000 '''(Rama can you check this figure in the GOC database? This is from our database, s Rama Balakrishnan, Rachael Huntley, David Hill, Harold Drabkin, Jane Lomax, Kimb
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  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Maria Costanzo, Selina Dwigh
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  • Rama and Paul have voiced concerns about processes that have some overlap with f AI: David will email Rama and Rachael to let them know about this. Each contributing annotation group
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  • ATTENDEES: Suzi, Paul T., Huaiyu, Donghui, Rama, David, Tanya, Chris, Jane, Heiko ===Single Step Process terms (Paul, Rama et al)===
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  • ...and Jane and David are on it, to coordinate what we're doing. Rachael and Rama are coordinating, but we have leeway on the ontology part. So let's just do
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  • Attendance:Chris, Judy, Jane, David, Mike, Kimberley, Pascale, Paul T., Rama, Suzi, Paul S. ...make it better organized. We can do more to educate people right up front. Rama has been heading up the team to rework things with Seth. GO-TOP will discus
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  • Rama will report on this in GOC meeting.
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  • * How often is the PAINT directory (filtered) updated in SVN? Rama will check into this.
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  • Rama and Rachael took pages on SVN and put into google spreadsheet to mark which Rama: can share list/spreadsheet with everyone to get additional input
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  • ** Rama- general guideline should be to annotate to specific term. If the authors s ** MikeC probably has this script. Rama will talk to MikeC.
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  • Present: Kimberly, Rama, Huaiyu, Rachael, Jane, Paul T. **Group from NTNU (Norway) in collaboration with Rama, Karen, Rachael, Judy et al. have submitted a paper on transcription factor
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  • ...general they are) after he's done with apoptosis re-curation; he'll email Rama about it. Chris might then look into automating at least part of the proces
    8 KB (1,210 words) - 11:50, 1 July 2014
  • |Rama Balakrishnan
    10 KB (1,551 words) - 07:53, 12 April 2019
  • *'''Present''': Rama, Pascale, David, Paul S., Kimberly, Rachael, Chris, Huaiyu, Jane, Suzi Rama, Chris - main task now is to move content across.
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  • ...ng and contrasting them. Includes gene annotation gold standard sets that Rama has been shepherding. Write our own gene enrichment tool. ...axed to allow Reactome IDs in the reference field? Person: Peter D’E and Rama.
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  • |Rama
    3 KB (373 words) - 05:00, 12 April 2019
  • **Rama: Now amigo2 is released, now we should make an announcement, and plan on a **Rama updated the wiki page, and will send out the format to the managers.
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  • ...://sourceforge.net/p/geneontology/ontology-requests/10258/ SF request from Rama] for a new term to annotate Rpt2, an ATPase of the regulatory particle (RP)
    3 KB (382 words) - 12:04, 15 July 2014
  • ** Drupal training/demo for adding content (Seth, Rama) Seth gave Rama a quick demo of the Drupal installation for the new Gene Ontology web site
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  • ** Rama- We don't want to confuse the users anymore by producing 2 GAFs. Proposal i
    3 KB (526 words) - 12:44, 9 April 2014
  • *Rachael and Rama to work on this
    2 KB (240 words) - 11:46, 27 June 2014
  • * Gene mania annotations still being discussed by Rama and Rachel - some concerns were brought up by email. * Rama has been discussing with people form the GeneMania group
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  • * Does BioGRID have the same kind of scoring system like IntAct? Rama: So far I don't think so, i will look into it. ...annotations is not looking for assigned_by in protein2GO. Rachael, Petra, Rama, Kimberley will talk about it separately (since this is a protein2GO issue
    3 KB (455 words) - 12:42, 9 April 2014
  • - Rachael and Rama's spreadsheet: [https://docs.google.com/spreadsheet/ccc?key=0AuvnWIcf9rbDdE
    5 KB (760 words) - 11:56, 1 July 2014
  • * Gene mania annotations still being discussed by Rama and Rachel - some concerns were brought up by email. * Rama has been discussing with people form the GeneMania group
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  • Val asked me (Rama) to give a refresher on where one should post what messages/questions. The Present: Rama, Paul, Edith, Janos, Petra, Kimberley, Judy, Harol, LI, Karen, Rachael, Jan
    6 KB (1,012 words) - 12:43, 9 April 2014
  • ...ouple of paint call, present a few families as examples. Huaiyu, Karen and Rama will probably do it.
    412 bytes (68 words) - 09:59, 8 April 2014
  • Present: David, Rama, Kimberly, Pascale, Jane, Paul S, Judy
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  • Rama
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  • Present: Suzi, Judy(for 10 min), PaulT, Huaiyu, Rama, Pascale, Jane, Kimberley, Rachael, David, Chris * MoonProt DB: Rama gave an overview of GO/how to make annotations to the MoonProt group over w
    2 KB (392 words) - 11:09, 27 June 2014
  • Present: Rama, Rachael, David, Kimberly, Chris, Pascale, Huaiyu, Judy, Suzi ...th/From column for IMP annotations to include paper identifiers. [Rachael, Rama]
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  • # Rama's request for a comment box.
    6 KB (1,061 words) - 12:00, 1 July 2014
  • |Rama |Rama
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  • ACTION: Rama set up new page for pubs ...th/From column for IMP annotations to include paper identifiers. [Rachael, Rama]
    5 KB (870 words) - 11:18, 27 June 2014
  • SGD: Rama, Edith, Diane
    5 KB (806 words) - 12:46, 9 April 2014
  • * Together with Rama Balakrishnan from SGD, Rachael Huntley is a manager for the GO Consortium's
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  • Present: Rama, Rachael, Pascale, Jane, Chris, Huaiyu, Kimberly, Paul T.
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  • * Email from the Transport Classification folks (Rama) Servers have been set up by Stuart and Rama is testing.
    4 KB (709 words) - 11:10, 27 June 2014
  • Rama Balakrishnan (SGD) Rama Balakrishnan, Rachael Huntley, Harold Drabkin, Jane Lomax, Kimberly Van Auk
    7 KB (1,102 words) - 11:53, 9 April 2014
  • In attendance: Chris, Fiona, Harold, Judy, Kimberly, Paul S., Petra, Rama, Sandra ...dance: Suzi, Judy, Paul S., Claire, Maria, Tony, Rachael, Chris, Kimberly, Rama, David, Harold
    6 KB (919 words) - 01:42, 16 April 2019
  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Maria Costanzo, Selina Dwigh
    11 KB (1,417 words) - 14:49, 10 December 2014
  • SGD: Rama, Stacia, Diane, Edith<br> ...roposed" on the documentation page. It should be changed to 'Implemented'. Rama will fix it.
    5 KB (804 words) - 12:32, 9 April 2014
  • ** Rama has talked R. Aramayo (Professor at Texas A&M) about submitting the annotat
    2 KB (397 words) - 10:40, 27 June 2014
  • SGD: Rama, Diane<br> Rama: aren't we being inconsistent here? When we reannotated the Txn factors, we
    4 KB (701 words) - 12:33, 9 April 2014
  • |colspan="1" | Ruth, Rachael, Donghui, Doug, Jennifer, Rama, Kimberly, Huaiyu, Dmitry, Judy |colspan="1" | Rachael, Rama, Suzi, Moni, Val anyone else who would like to become involved
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  • *In attendance: Judy, Suzi, Mike, Paul T., Jane, Rachael, David, Kimberly, Rama, Huaiyu **Rama would like to submit an abstract on the GPAD/GPI file format
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  • SGD: Rama, Diane, Paul<br>
    4 KB (622 words) - 12:30, 9 April 2014
  • SGD: Rama, Selina, Diane, Stacia<br>
    5 KB (800 words) - 12:30, 9 April 2014
  • * Together with Rama Balakrishnan from SGD, Rachael Huntley is a manager for the GO Consortium's
    14 KB (1,963 words) - 05:50, 13 October 2014
  • Rama Balakrishnan (SGD) Rama Balakrishnan, Rachael Huntley, Harold Drabkin, Jane Lomax, Kimberly Van Auk
    5 KB (808 words) - 11:46, 9 April 2014
  • Present: Rama, Chris, David, Jane, Kimberley, Pascale, Suzi
    2 KB (347 words) - 05:50, 15 April 2019
  • SGD: Rama, Selina, Stacia, Diane, Edith<br> ===Hardware changes (Rama)===
    7 KB (1,151 words) - 05:48, 15 April 2019
  • ...d in a discussion between Alan Bridge, Pascale Gaudet, Rachael Huntley and Rama Balakrishnan during 2012.
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  • Present: Rama, Li, Moni, Suzi, Huaiyu, Karen * Rama said that it was OK for users to add the link to the page.
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  • SGD: Rama,Paul, Diane, Edith<br>
    3 KB (484 words) - 05:48, 15 April 2019
  • Participants: Karen, Rama, Li, Donghui, Suzi, Paul T, Huaiyu *Rama: Val just completed the fission yeast cell cycle pathway. David (Suzi point
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  • Participants: Rama, Karen, Pascale, Moni, Huaiyu
    1 KB (220 words) - 13:51, 22 April 2014
  • SGD: Rama, Paul, Diane<br>
    4 KB (731 words) - 05:48, 15 April 2019
  • Participants: Rama, Donghui, Paul T, Moni, Judy, Kimberley, Suzi, Huaiyu, Pascale, Karen, Chri *Rama and Judy - More useful and efficient to have everyone together in the same
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  • * Rama Balakrishnan Stanford University (arriving on 12th at 735PM by United)
    6 KB (799 words) - 05:11, 13 October 2014
  • Rama Balakrishnan (SGD) Rama Balakrishnan, Rachael Huntley, Harold Drabkin, Jane Lomax, Kimberly Van Auk
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  • Participants: Rama, Donghui, Moni, Kimberley, Suzi, Huaiyu, Pascale, Li, Paul T ...week of July 28 (28-31). It is likely to be at SGD office at Porter Drive. Rama is going to confirm with Mike. Once the venue is confirmed, Huaiyu will sen
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  • Present: Rama, Huaiyu, Paul T., Kimberly, Pascale, David, Rachael, Judy Rama: Drupal site moved to Amazon cloud (lowest tier)
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  • ...the Evidence Ontology (ECO)." Marcus C. Chibucos, Christopher J. Mungall, Rama Balakrishnan, Karen R. Christie, Rachael P. Huntley, Owen White, Judith A. * Together with Rama Balakrishnan from SGD, Rachael Huntley is a manager for the GO Consortium's
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  • ** Drupal Content: migration complete (Moni, Seth, Rama, ...) ** AmiGO 2.1 in testing May (Seth, Rama)
    4 KB (484 words) - 06:58, 18 June 2014
  • Rama Balakrishnan
    13 KB (2,084 words) - 07:55, 12 April 2019
  • ...tps://trello.com/c/OfHYkQCl/99-review-google-analytics-data trello]) (Seth/Rama) #* GO annotation (Rama) [[File:IntActGO.pptx]]
    10 KB (1,354 words) - 06:53, 31 August 2015
  • ** Action: Rama to bring this as a discussion for the Ontology and annotation groups.
    3 KB (463 words) - 07:36, 27 June 2014
  • ...u find you need to use this for MF, bring up your example with Rachael and Rama, or request a new GO term.
    18 KB (2,857 words) - 09:11, 10 October 2014
  • SGD: Rama, Edith, Diane * not_happens_during- there is one SGD annotation with this relationship. Rama will check into how this can be reannotated.
    7 KB (1,194 words) - 05:48, 15 April 2019
  • Attending: Suzi, Chris, Rama, David H, Huaiyu, Jane, Kimberly
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  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Maria Costanzo, Selina Dwigh
    5 KB (795 words) - 12:56, 1 July 2014
  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Maria Costanzo, Selina Dwigh
    5 KB (666 words) - 12:56, 1 July 2014
  • SGD: Rama, Edith, Stacia <br>
    3 KB (468 words) - 05:47, 15 April 2019
  • Participants: Li, Suzi, Moni, Donghui, Pascale, Karen, Rama *PAINT jamboree participants: Li, Karen, Donghui, Rama, Moni, Huaiyu, Pascale, Mark. Kimberly (?)
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  • SGD: Rama, Diane, Edith <br>
    7 KB (1,104 words) - 05:46, 15 April 2019
  • Participants: Li, Rama, Karen, Judy, Paul, Suzi, Huaiyu *Karen and Rama said they had to check the schedule with their families.
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  • ===PAINT (Rama)=== * Rama is writing a small blurb about the biological phase term for the GOC websit
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  • Rama emailed the editors on March 26: Discuss, decide, reply to Rama.
    3 KB (426 words) - 08:20, 2 April 2015
  • Present: Rama, Judy, David, Jane, Tanya, Pascale, Suzi, Moni, Chris, DavidOS, Prudence, S
    2 KB (283 words) - 05:46, 15 April 2019
  • Participants: Rama, Karen, Suzi, Huaiyu, Moni, Chris, Pascale *Both Karen and Rama said they liked the current trees with regard to the number of genomes.
    2 KB (432 words) - 15:08, 11 December 2014
  • Judy, Suzi, Chris, Rama, Pascale, Kimberly, David, Paul T. *Moni is working with Rachael and Rama on documentation for submitting annotations
    3 KB (541 words) - 05:50, 15 April 2019
  • *Rama: protein2go displays ECO code for evidence. Currently Marcus is the only pe *Rama: We also need a mechanism to alert curators about new ECO codes so we know
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  • Present: Rama, Rachael, Judy, Suzi, Li, Kimberly, Petra, Paola, Aleks, Jane, Susan T, bec * Rama will check with Heiko/Chris about empty GAF files. Also document how to run
    5 KB (793 words) - 05:48, 15 April 2019
  • Participants: Karen, Suzi, Judy, Paul T. Huaiyu, Rama, Moni.
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  • Present: Rama, Rachael, David Hill, Ruth, Becky, Paul, Li, Petra, Paola, Aleks, Kimberly, * Regarding running the GAF check ourselves, Rama will check with Heiko and write some documentation. This needs setting up O
    3 KB (504 words) - 05:48, 15 April 2019
  • Participants: Huaiyu, Paul T., Pascale, Rama, Karen
    1 KB (213 words) - 15:08, 11 December 2014
  • Participants: Donghui, Suzi, Paul T., Moni, Karen, Chris, Rama, Mark, Pascale, Li, Huaiyu
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  • Hi Rama,
    1 KB (253 words) - 05:51, 15 April 2019
  • In attendance: Rama, Moni, Suzi, Edith, Kimberly, Midori, Donghui, Stacia, Pascale, Rachael, Pr ***Rama - submitted a github ticket for this, but will need to follow up with Heik
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  • Participants: Pascale, Marc, Huaiyu, Karen, Paul, Suzi, Moni, Li, Rama
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  • Rama Balakrishnan (SGD)
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  • * Annotation (Rama) ...on group one option is to give Rama extra powers with protein2GO. Pascale, Rama and Kimberly will come up with a list of tasks that we need power for. This
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  • ===Making positive annotation when there is a Not annotation (rama)===
    6 KB (954 words) - 05:46, 15 April 2019
  • Participants: Rama, Donghui, Li, Moni, Pascale, Suzi, Chris, Paul, Huaiyu
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  • Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Maria Costanzo, Janos Demete * Marcus C. Chibucos, Christopher J. Mungall, '''Rama Balakrishnan''', Karen R. Christie, Rachael P. Huntley, Owen White1, Judith
    6 KB (887 words) - 12:58, 17 December 2014
  • Present: Rama, Kimberly, Chris, David, Huaiyu, PaulT, Suzi * In the context of the Pho80-85 pathway that Rama showed (http://go-genkisugi.rhcloud.com/seed/model/gomodel:sgd-536d71c50000
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  • ** Staff: Rama Balakrishnan, Rachael Huntley, Monica Muñoz-Torres, Harold Drabkin, Jane L
    4 KB (604 words) - 13:06, 19 December 2014
  • Participants: Rama, Chris, Suzi, Pascale, Paul T., Karen, Li, Huaiyu *Rama pointed out that this actually happened quite often.
    4 KB (771 words) - 11:31, 6 January 2015
  • Get Kimberly and Rama on board, LEGO call?
    6 KB (975 words) - 09:58, 13 January 2015
  • * Rama - is there an option to clone a model? Chris: not at the moment. We have to * Rama- the relaionship text box expects us to start typing and will auto-suggest
    3 KB (440 words) - 13:22, 7 January 2015
  • Present: Rama, Jane, Becky, Paola, Aleks, Tanya, Chris, Suzi, Pascale, Kimberly, Edith, S ...enough) so people can raise their hands on a chat window to make comments. Rama will look into holding these calls via bluejeans (Stanford account).
    2 KB (378 words) - 14:10, 16 January 2015
  • Participants: Suzi, Paul T, Moni, Huaiyu, Rama, Karen ===NOT annotation question from Rama===
    2 KB (366 words) - 09:08, 20 January 2015
  • * Rama will look into adding more details to this pathway by next meeting. * Rama- how is this tool going to be used by curators? Curator time is limited and
    1 KB (181 words) - 13:58, 2 February 2015
  • Participants: Rama, Moni, Karen, Marc, Pascale, Huaiyu * Rama raised the question about refGenome in col 15 in PAINT gaf files. Refgenome
    839 bytes (141 words) - 15:33, 20 February 2015
  • Present: Rama, Chris, Paola, Suzi, Judy, PaulT, Kimberly, Huaiyu ...mone to swimming behavior. They claim the sheep growth hormone is similar Rama will talk to agbase folks to clarify before we discuss this further.
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  • Request from Rama based on this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806484/
    2 KB (242 words) - 08:32, 26 February 2015
  • Participants: Rama, Pascale, Marc, Paul T., Moni, Karen, Huaiyu * Rama: The reannotation actually took quite a lot of time.
    3 KB (417 words) - 05:45, 9 April 2019
  • *On call: Chris, Huaiyu, Paola, Rama, Kimberly, Judy, David, Paul T., Pascale **Kimberly, Rama:
    3 KB (553 words) - 05:50, 15 April 2019
  • ...vid H’s plan (approved): we explain this on an annotation call; (update: Rama suggested April) we can suggest to look specifically at TRP channels, but o
    8 KB (1,246 words) - 02:53, 11 May 2015
  • #* Rama, David OS, Chris #* Chris, Seth, Mike, Rama
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  • * Here are the links to the models built by David, Kimberly and Rama Rama- http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc00
    3 KB (538 words) - 07:32, 13 May 2015
  • Rama reminded us that we should reply to this user [now done]:
    8 KB (1,247 words) - 12:24, 10 March 2015
  • Participants: Rama, Karen, Pascale, Suzi, Marc, Janos, Huaiyu Paul T.
    3 KB (450 words) - 08:57, 7 March 2019
  • Present: PaulT, Heiko, Rama, Kimberly, Huaiyu
    600 bytes (95 words) - 14:01, 3 March 2015
  • | Rama Balakrishnan
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  • Participants: Marc, Karen, Li, Chris, Huaiyu, Rama, Paul T., Moni *: - At the last PAINT meeting, during discussion of Rama's question about use of the "Ref Genome" versus "GO Central" sources, Suzi
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  • ...s they should be. But it is not clear if col-16 data are also transferred. Rama will check with Chris.
    4 KB (652 words) - 13:22, 24 March 2015
  • Participants: Li, Rama, Suzi, Moni, Huaiyu, Donghui, Paul T., Chris *: - At the last PAINT meeting, during discussion of Rama's question about use of the "Ref Genome" versus "GO Central" sources, Suzi
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  • ...y. It is not a lot of time, but we have run similar meetings successfully. Rama has some contacts for autophagy. Paola will let us know when we have update
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  • Attendees:Rama, Harold, DavidOS, Paola, Rama, Heiko, DavidH, PaulT Copying from last week - we need to discuss more today, and Rama will join us:
    8 KB (1,307 words) - 08:33, 16 April 2015
  • ...r how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebe
    16 KB (2,263 words) - 08:32, 21 August 2015
  • | Rama Balakrishnan
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  • ...the non-specific (and specific?) channels, and we will take it from there. Rama will distribute the list/post it on the wiki. * <font color="red">Action item</font>Rama will send out a break down of annotations to these terms (by group) and we
    7 KB (1,040 words) - 14:17, 12 May 2015
  • Participants: Donghui, Karen, Rama, Marc, Huaiyu, Moni, Li
    5 KB (657 words) - 08:56, 7 March 2019
  • ...r how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebe ** Rama: I would like to consult other curation projects: e.g. bioGRID to see how t
    17 KB (2,851 words) - 01:52, 27 May 2015
  • * David, Kimberly, and Rama will review their March paper models to compare with Paul's version.
    4 KB (697 words) - 10:08, 19 May 2015
  • '''Participants''': Marc, Pascale, Paul, Karen, Moni, Chris, Rama, Janos, Li, and Huaiyu (left early),
    7 KB (1,129 words) - 08:56, 7 March 2019
  • ==GAF2.1 (addition of pipe/comma to With/From column) (Rama)== * Rama: there are some outside users who have tickets in SF. How do we handle thos
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  • * Rama: remove publications guidelines from main GO website * Rama: add publication guidelines in the wiki (with a disclaimer that this is int
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  • Present: Rama, Birgit, Sandra, JudyB, Harold, Kimberly, Chris, Ruth, Pascale * Rama: Considering that you guys and protein2GO are neighbors, why aren't you usi
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  • Rama presented family PTHR23100. She had 2 issues, otherwise the family was stra
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  • This feature was a suggestion from a previous call and Rama made a ticket in github to make sure it is not lost. protein2GO can easily * Rama: different groups annotate differently. the goal of this exercise is to go
    12 KB (1,793 words) - 15:40, 23 June 2015
  • ===Minting DOIs for GO_REFs (Rama)=== ===Obsoleting relationships (Rama)===
    4 KB (663 words) - 13:16, 15 July 2015
  • ...sues, but no editors are involved - maybe DOS could liaise with Birgit and Rama?
    4 KB (675 words) - 11:48, 9 July 2015
  • Ruth Lovering, Rama Balakrishnan, Tanya Berardini, Judith Blake, Karen Christie, Harold Drabkin
    82 KB (12,252 words) - 10:44, 23 March 2020
  • * Rama: It doesn't make sense to make a Process annotation with IPI. Just because
    8 KB (1,301 words) - 01:27, 20 July 2015
  • RAMA notes that those not using protein2go may not be getting warnings about inc AI: Rama to check with Tony about who is getting reports of failure to load into Qui
    25 KB (3,988 words) - 13:59, 29 July 2015
  • ...stions about age of respondents as for are uninformative for our purposes. Rama has a script that collects authors names from publications mentioning GO an
    1 KB (184 words) - 13:16, 15 July 2015
  • ...sues, but no editors are involved - maybe DOS could liaise with Birgit and Rama?
    5 KB (796 words) - 02:55, 5 August 2015
  • '''Participants''': Janos, Rama, Huaiyu, Paul T, Suzi
    2 KB (343 words) - 08:56, 7 March 2019
  • ** Rama: is the taxon ID for a specific strain/Ref.proteome or the generic taxon id ** Rama: while we are renaming files we should rename the GOA files too. For e.g. t
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  • '''Participants''': Rama, Moni, Karen, Huaiyu, Pascale, Marc
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  • Chris: Rama was looking at this.
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  • * 9:30 - 11:00 '''Workshop #1''': Annotation (Rama, Pascale, David OS, Chris, Rachael, Ruth) - Room 309
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  • Rama: How to represent PS in this case? check if there are recent papers explain Rama: A NOT qualifier will change the meaning of hte annotation. If you annotate
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  • *In attendance: Paola, Kimberly, Judy, Paul T., Rama, David, Chris, Huaiyu, Suzi, Melanie, Moni
    4 KB (628 words) - 09:41, 19 August 2015
  • ** Rama mentioned that she and PaulT worked on a model for the March annotation con
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  • '''Participants''': Rama, Pascale, Marc, Karen, Donghui, Huaiyu, Paul T. Suzi
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  • ** Rama: one option is to post a message on the go-consortium list about the relati
    9 KB (1,438 words) - 14:51, 27 August 2015
  • #*Rama and David H would like to also, but both of them have busy schedule, so not * Ruth and Val to help Moni (+ perhaps Rama & Melanie) with composing the answer page for groups wishing to provide ann
    9 KB (1,534 words) - 12:18, 16 September 2015
  • ** Heiko is going to implement the checks in Jenkins. Rama will get a list of these checks from Tony and pass them along.
    10 KB (1,284 words) - 10:41, 22 September 2015
  • ...s the author of paper citing GO, we selected you to answer this survey”. Rama will send example. ** From Rama: there are two working groups on Complexes: first one to come up with guide
    7 KB (1,187 words) - 09:57, 8 October 2015
  • Attendance: Rama, David H., Paul T., Kimberly, Seth, Chris, Heiko
    2 KB (295 words) - 08:42, 21 September 2015
  • On call: Chris, David, Heiko, Kimberly, Paul T., Rama, Seth
    1 KB (195 words) - 07:17, 19 October 2015
  • Rama Balakrishnan (SGD) - thru mid-October 2015; David Hill (MGI) and Kimberly V Rama Balakrishnan worked with Trey Idekar's group (UCSD) on identifying missing
    5 KB (746 words) - 21:39, 7 December 2015
  • *We used to use Bluejeans, administered by Rama ==Replacing Rama==
    5 KB (817 words) - 08:00, 21 October 2015
  • *Rama had been maintaining the help desk schedule and turned that over to Tanya w **Rama (SGD) - 4 weeks (no longer here)
    4 KB (757 words) - 09:12, 2 December 2015
  • ...: '''Kimberly''' offered example about a group wants to annotate lncRNAs - Rama started working with them. They have protein-to-GO accounts. '''Moni''': Tr
    10 KB (1,701 words) - 05:59, 9 April 2019