https://wiki.geneontology.org/api.php?action=feedcontributions&user=Maria&feedformat=atomGO Wiki - User contributions [en]2024-03-28T12:30:06ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Gohelp_rota&diff=57097Gohelp rota2015-05-18T18:34:58Z<p>Maria: </p>
<hr />
<div>[[Category:Advocacy and Outreach]]<br />
*'''Paola''': Week beginning 4th May<br />
*'''Donghui''': Week beginning 11th May<br />
*'''Moni''': Week beginning 18th May<br />
*'''MariaC''': Week beginning 25th May<br />
*'''Harold''': Week beginning 1st June<br />
*'''Tanya''': Week beginning 8th June<br />
*'''Edith''': Week beginning 15th June<br />
*'''Rebecca(UCL)''': Week beginning 22nd June<br />
*'''Kimberly''': Week beginning 29th June<br />
*'''Rama''': Week beginning 29th June<br />
*'''Moni''': Week beginning 6th July<br />
*'''David OS''': Week beginning 13th July<br />
*'''Harold''': Week beginning 20th July<br />
*'''Victoria(RGD)''': Week beginning 27th July<br />
*'''Rama''': Week beginning 3rd August<br />
*'''Paola''': Week beginning 10th August (swapped with Tanya; I was up for wc Aug 24th)<br />
*'''Petra(Dicty)''': Week beginning 17th August<br />
*'''Tanya''': Week beginning 24th August (swapped with Paola)<br />
*'''MariaC''': Week beginning 31st August<br />
<br />
<br />
Victoria, Petra, Helen(Fly), Rachael, Becky have offered to be on the rotation 2x a year.<br />
<br><br />
<br />
At the end of your shift, please send a reminder email to the next person on the list to remind them that it's their turn. Thanks.<br />
<br />
[[Gohelp|GO help main page]]<br />
<br />
The software rota is concurrent with the main rota:<br />
<br />
[[Gohelp_software_rota]]<br />
<br />
[[JIRA issues|GO-Help JIRA issues]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Gohelp&diff=56077Gohelp2015-02-19T17:28:51Z<p>Maria: /* Help with queries */</p>
<hr />
<div>'''Starting July 1, 2013'''<br />
<br />
All queries to the GO helpdesk (via the webform or by email) to the address '''go-helpdesk(-at-)geneontology[-dot-]org''' will be routed to the new GOJIRA system:<br />
<br />
[http://jira.geneontology.org http://jira.geneontology.org]<br />
<br />
If you don't have a login, email tberardini(at)arabidopsis(dot)org to request one.<br />
<br />
There's a section on 'Help with queries' at the bottom of this wiki.<br />
<br />
'''Summary of duties of a GO helper (see below for details)'''<br />
<br />
- Triage queries. Assign queries to others or to yourself. Resolve queries assigned to you if any.<br />
<br />
- Check the [http://geneontology.org/faq-page FAQ]. Answers might already be there.<br />
<br />
- If needed, improve FAQ documentation on website, or assign task to others (contact Seth or Moni if you need help with the website).<br />
<br />
- Post on the website: interesting papers that use GO, significant updates to annotation files and to ontology structure/content, etc.<br />
<br />
- At the end of your weekly shift, wrap up pending queries, following up with assignees if necessary, or otherwise make sure that queries can be closed. Then send a reminder to the next person on the rota. <br />
<br />
=Process=<br />
'''Starting July 1, 2013'''<br />
<br />
To divide up the work of answering gohelp queries, we use a <b>[[gohelp rota]]</b> where each person is 'on duty' for 1 week at a time. It is responsibility of the person on duty to make sure that all queries are answered, either by answering it themselves, or by assigning the issue to someone else to answer.<br />
<br />
All helpdesk questions will be handled through GOJIRA http://jira.geneontology.org<br />
<br />
When a new issue comes in, you will receive an email from GOJIRA.<br />
<br />
*Log in to your account. <br />
<br />
*Work your way through the open and unassigned issues.<br />
<br />
'''For each one:'''<br />
<br />
*Click on the Summary field and change the Summary to something descriptive. (no email generated)<br />
<br />
*Click on the Edit button and <br />
**(1) Select an Issue Type (Bug Report, New Feature Request, Question, Spam/Delete) (no email generated)<br />
**(2) Add one or more Components (annotations, internal discussion, ontology, out of scope for GO, software, third party tools, website) (no email generated) Leave Labels alone, we don't use these.<br />
**(3) '''Do not''' add your response to the user in the comment box on this popped-out window. The comment '''will not be sent''' to the user if you do this.<br />
<br />
*Decide, can you answer this issue yourself? <br />
**IF YES: Assign the issue to yourself. Click on the “Update” button in the lower right corner of the pop-up window to update and close the Edit window. Then click on the 'Comment' button at the bottom left hand corner of the page and answer the question using the comment section of the webpage. Your comment '''will be sent''' to the user (the reporter), yourself (if you've set your profile preferences that way), and all go-helpers.<br />
**IF NO: Assign the issue to someone else (if software related, assign to GO Software) who should answer the question. Then click on the “Update” button in the lower right corner of the pop-up window to update and close the Edit window. Click on the 'Comment' button at the bottom left hand corner of the page to send a reply to the user, saying something like "Thanks for contacting GO. I'm passing your question on to…". If the person you want to assign the issue to is not on the list of JIRA users (doesn't show up when you start typing their name in the box), please let me (Tanya) know and I'll add them.<br />
<br />
*Want to make an 'internal' comment that is not seen by the issue reporter?<br />
**At the bottom of the Comment window, there is a little padlock that is unlocked and says 'Viewable by All Users' by default. From the padlock's drop-down menu, select 'go-curators' and the comment will be seen by all people on the go rota as well as Judy, Suzi, Mike, Seth, Chris, and Heiko. The padlock will appear locked after you choose this option.<br />
<br />
*Please make sure you check your issues on the JIRA website for any additional correspondence from the submitter, in addition to monitoring your email inboxes. (If submitters attach files to their replies, these will be threaded in Jira, but no emails to GO people will be generated.)<br />
<br />
At the end of the week, close any items assigned to yourself that require no further action. You may want to ping people who you've assigned issues to if they haven't responded yet. (Spam/Delete issues will be deleted by either Bob or Tanya.)<br />
<br />
=Setting GOJIRA preferences=<br />
<br />
'''JIRA's default setting is to not notify users of their own changes. This can be changed on a per user basis via their Profile Preferences.'''<br />
<br />
Each user can set this if he or she wants to get email notifications for "Current User". It's off by default. 'Off' means that if you comment on an issue, you WILL NOT receive a copy of the comment by email. Some of you may want to change that behavior.<br />
<br />
Go to your User display by clicking on your username in any page. Click on "Profile". Go to the Preferences section. Click on the little pencil button off to the right to edit preferences. Set "My Changes" to "Notify me". The Profile section is also where you can set the email prefs for HTML vs. Text. I know that some of you prefer to receive the emails as Text.<br />
<br />
Go to your Dashboard (what you see when you log in). In the 'Favorite Filters' section, click on Manage Filters. Select both<br />
'Open Issues' and 'Unassigned Open Issues' from the choices. This will then show you by default the number of issues in each category when you log in and you can then click to each list individually.<br />
<br />
=Help with queries=<br />
<br />
*There is a [[gohelp people list]] of the best people to assign the different queries to.<br />
<br />
* For problems with GO term enrichment, also forward the email to go-software@lists.stanford.edu to reach programmers who are not on go-help.<br />
<br />
*The archive from the old mailman system is still available for searching: [https://mailman.stanford.edu/pipermail/go-helpdesk/].<br />
<br />
*The EBI gohelp JIRA set up is also still available for searching: [https://www.ebi.ac.uk/panda/jira/browse/GOHELP]<br />
<br />
[[Category:Advocacy and Outreach]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Gohelp&diff=56076Gohelp2015-02-19T17:28:25Z<p>Maria: /* Help with queries */</p>
<hr />
<div>'''Starting July 1, 2013'''<br />
<br />
All queries to the GO helpdesk (via the webform or by email) to the address '''go-helpdesk(-at-)geneontology[-dot-]org''' will be routed to the new GOJIRA system:<br />
<br />
[http://jira.geneontology.org http://jira.geneontology.org]<br />
<br />
If you don't have a login, email tberardini(at)arabidopsis(dot)org to request one.<br />
<br />
There's a section on 'Help with queries' at the bottom of this wiki.<br />
<br />
'''Summary of duties of a GO helper (see below for details)'''<br />
<br />
- Triage queries. Assign queries to others or to yourself. Resolve queries assigned to you if any.<br />
<br />
- Check the [http://geneontology.org/faq-page FAQ]. Answers might already be there.<br />
<br />
- If needed, improve FAQ documentation on website, or assign task to others (contact Seth or Moni if you need help with the website).<br />
<br />
- Post on the website: interesting papers that use GO, significant updates to annotation files and to ontology structure/content, etc.<br />
<br />
- At the end of your weekly shift, wrap up pending queries, following up with assignees if necessary, or otherwise make sure that queries can be closed. Then send a reminder to the next person on the rota. <br />
<br />
=Process=<br />
'''Starting July 1, 2013'''<br />
<br />
To divide up the work of answering gohelp queries, we use a <b>[[gohelp rota]]</b> where each person is 'on duty' for 1 week at a time. It is responsibility of the person on duty to make sure that all queries are answered, either by answering it themselves, or by assigning the issue to someone else to answer.<br />
<br />
All helpdesk questions will be handled through GOJIRA http://jira.geneontology.org<br />
<br />
When a new issue comes in, you will receive an email from GOJIRA.<br />
<br />
*Log in to your account. <br />
<br />
*Work your way through the open and unassigned issues.<br />
<br />
'''For each one:'''<br />
<br />
*Click on the Summary field and change the Summary to something descriptive. (no email generated)<br />
<br />
*Click on the Edit button and <br />
**(1) Select an Issue Type (Bug Report, New Feature Request, Question, Spam/Delete) (no email generated)<br />
**(2) Add one or more Components (annotations, internal discussion, ontology, out of scope for GO, software, third party tools, website) (no email generated) Leave Labels alone, we don't use these.<br />
**(3) '''Do not''' add your response to the user in the comment box on this popped-out window. The comment '''will not be sent''' to the user if you do this.<br />
<br />
*Decide, can you answer this issue yourself? <br />
**IF YES: Assign the issue to yourself. Click on the “Update” button in the lower right corner of the pop-up window to update and close the Edit window. Then click on the 'Comment' button at the bottom left hand corner of the page and answer the question using the comment section of the webpage. Your comment '''will be sent''' to the user (the reporter), yourself (if you've set your profile preferences that way), and all go-helpers.<br />
**IF NO: Assign the issue to someone else (if software related, assign to GO Software) who should answer the question. Then click on the “Update” button in the lower right corner of the pop-up window to update and close the Edit window. Click on the 'Comment' button at the bottom left hand corner of the page to send a reply to the user, saying something like "Thanks for contacting GO. I'm passing your question on to…". If the person you want to assign the issue to is not on the list of JIRA users (doesn't show up when you start typing their name in the box), please let me (Tanya) know and I'll add them.<br />
<br />
*Want to make an 'internal' comment that is not seen by the issue reporter?<br />
**At the bottom of the Comment window, there is a little padlock that is unlocked and says 'Viewable by All Users' by default. From the padlock's drop-down menu, select 'go-curators' and the comment will be seen by all people on the go rota as well as Judy, Suzi, Mike, Seth, Chris, and Heiko. The padlock will appear locked after you choose this option.<br />
<br />
*Please make sure you check your issues on the JIRA website for any additional correspondence from the submitter, in addition to monitoring your email inboxes. (If submitters attach files to their replies, these will be threaded in Jira, but no emails to GO people will be generated.)<br />
<br />
At the end of the week, close any items assigned to yourself that require no further action. You may want to ping people who you've assigned issues to if they haven't responded yet. (Spam/Delete issues will be deleted by either Bob or Tanya.)<br />
<br />
=Setting GOJIRA preferences=<br />
<br />
'''JIRA's default setting is to not notify users of their own changes. This can be changed on a per user basis via their Profile Preferences.'''<br />
<br />
Each user can set this if he or she wants to get email notifications for "Current User". It's off by default. 'Off' means that if you comment on an issue, you WILL NOT receive a copy of the comment by email. Some of you may want to change that behavior.<br />
<br />
Go to your User display by clicking on your username in any page. Click on "Profile". Go to the Preferences section. Click on the little pencil button off to the right to edit preferences. Set "My Changes" to "Notify me". The Profile section is also where you can set the email prefs for HTML vs. Text. I know that some of you prefer to receive the emails as Text.<br />
<br />
Go to your Dashboard (what you see when you log in). In the 'Favorite Filters' section, click on Manage Filters. Select both<br />
'Open Issues' and 'Unassigned Open Issues' from the choices. This will then show you by default the number of issues in each category when you log in and you can then click to each list individually.<br />
<br />
=Help with queries=<br />
<br />
*There is a [[gohelp people list]] of the best people to assign the different queries to.<br />
<br />
* For problems with GO term enrichment, also forward the email to go-software@lists.stanford.edu to reach programmers that are not on go-help.<br />
<br />
*The archive from the old mailman system is still available for searching: [https://mailman.stanford.edu/pipermail/go-helpdesk/].<br />
<br />
*The EBI gohelp JIRA set up is also still available for searching: [https://www.ebi.ac.uk/panda/jira/browse/GOHELP]<br />
<br />
[[Category:Advocacy and Outreach]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Gohelp&diff=56069Gohelp2015-02-19T16:35:03Z<p>Maria: /* Process */</p>
<hr />
<div>'''Starting July 1, 2013'''<br />
<br />
All queries to the GO helpdesk (via the webform or by email) to the address '''go-helpdesk(-at-)geneontology[-dot-]org''' will be routed to the new GOJIRA system:<br />
<br />
[http://jira.geneontology.org http://jira.geneontology.org]<br />
<br />
If you don't have a login, email tberardini(at)arabidopsis(dot)org to request one.<br />
<br />
There's a section on 'Help with queries' at the bottom of this wiki.<br />
<br />
'''Summary of duties of a GO helper (see below for details)'''<br />
<br />
- Triage queries. Assign queries to others or to yourself. Resolve queries assigned to you if any.<br />
<br />
- Check the [http://geneontology.org/faq-page FAQ]. Answers might already be there.<br />
<br />
- If needed, improve FAQ documentation on website, or assign task to others (contact Seth or Moni if you need help with the website).<br />
<br />
- Post on the website: interesting papers that use GO, significant updates to annotation files and to ontology structure/content, etc.<br />
<br />
- At the end of your weekly shift, wrap up pending queries, following up with assignees if necessary, or otherwise make sure that queries can be closed. Then send a reminder to the next person on the rota. <br />
<br />
=Process=<br />
'''Starting July 1, 2013'''<br />
<br />
To divide up the work of answering gohelp queries, we use a <b>[[gohelp rota]]</b> where each person is 'on duty' for 1 week at a time. It is responsibility of the person on duty to make sure that all queries are answered, either by answering it themselves, or by assigning the issue to someone else to answer.<br />
<br />
All helpdesk questions will be handled through GOJIRA http://jira.geneontology.org<br />
<br />
When a new issue comes in, you will receive an email from GOJIRA.<br />
<br />
*Log in to your account. <br />
<br />
*Work your way through the open and unassigned issues.<br />
<br />
'''For each one:'''<br />
<br />
*Click on the Summary field and change the Summary to something descriptive. (no email generated)<br />
<br />
*Click on the Edit button and <br />
**(1) Select an Issue Type (Bug Report, New Feature Request, Question, Spam/Delete) (no email generated)<br />
**(2) Add one or more Components (annotations, internal discussion, ontology, out of scope for GO, software, third party tools, website) (no email generated) Leave Labels alone, we don't use these.<br />
**(3) '''Do not''' add your response to the user in the comment box on this popped-out window. The comment '''will not be sent''' to the user if you do this.<br />
<br />
*Decide, can you answer this issue yourself? <br />
**IF YES: Assign the issue to yourself. Click on the “Update” button in the lower right corner of the pop-up window to update and close the Edit window. Then click on the 'Comment' button at the bottom left hand corner of the page and answer the question using the comment section of the webpage. Your comment '''will be sent''' to the user (the reporter), yourself (if you've set your profile preferences that way), and all go-helpers.<br />
**IF NO: Assign the issue to someone else (if software related, assign to GO Software) who should answer the question. Then click on the “Update” button in the lower right corner of the pop-up window to update and close the Edit window. Click on the 'Comment' button at the bottom left hand corner of the page to send a reply to the user, saying something like "Thanks for contacting GO. I'm passing your question on to…". If the person you want to assign the issue to is not on the list of JIRA users (doesn't show up when you start typing their name in the box), please let me (Tanya) know and I'll add them.<br />
<br />
*Want to make an 'internal' comment that is not seen by the issue reporter?<br />
**At the bottom of the Comment window, there is a little padlock that is unlocked and says 'Viewable by All Users' by default. From the padlock's drop-down menu, select 'go-curators' and the comment will be seen by all people on the go rota as well as Judy, Suzi, Mike, Seth, Chris, and Heiko. The padlock will appear locked after you choose this option.<br />
<br />
*Please make sure you check your issues on the JIRA website for any additional correspondence from the submitter, in addition to monitoring your email inboxes. (If submitters attach files to their replies, these will be threaded in Jira, but no emails to GO people will be generated.)<br />
<br />
At the end of the week, close any items assigned to yourself that require no further action. You may want to ping people who you've assigned issues to if they haven't responded yet. (Spam/Delete issues will be deleted by either Bob or Tanya.)<br />
<br />
=Setting GOJIRA preferences=<br />
<br />
'''JIRA's default setting is to not notify users of their own changes. This can be changed on a per user basis via their Profile Preferences.'''<br />
<br />
Each user can set this if he or she wants to get email notifications for "Current User". It's off by default. 'Off' means that if you comment on an issue, you WILL NOT receive a copy of the comment by email. Some of you may want to change that behavior.<br />
<br />
Go to your User display by clicking on your username in any page. Click on "Profile". Go to the Preferences section. Click on the little pencil button off to the right to edit preferences. Set "My Changes" to "Notify me". The Profile section is also where you can set the email prefs for HTML vs. Text. I know that some of you prefer to receive the emails as Text.<br />
<br />
Go to your Dashboard (what you see when you log in). In the 'Favorite Filters' section, click on Manage Filters. Select both<br />
'Open Issues' and 'Unassigned Open Issues' from the choices. This will then show you by default the number of issues in each category when you log in and you can then click to each list individually.<br />
<br />
=Help with queries=<br />
<br />
*There is a [[gohelp people list]] of the best people to assign the different queries to.<br />
<br />
*The archive from the old mailman system is still available for searching: [https://mailman.stanford.edu/pipermail/go-helpdesk/].<br />
<br />
*The EBI gohelp JIRA set up is also still available for searching: [https://www.ebi.ac.uk/panda/jira/browse/GOHELP]<br />
<br />
[[Category:Advocacy and Outreach]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Gohelp_rota&diff=55873Gohelp rota2015-01-20T15:58:40Z<p>Maria: </p>
<hr />
<div>[[Category:Advocacy and Outreach]]<br />
*'''Harold''': Week beginning 5th January<br />
*'''Donghui''': Week beginning 12th January<br />
*'''Moni''': Week beginning 19th January<br />
*'''Edith''': Week beginning 26th January<br />
*'''Paola''': Week beginning 2nd February<br />
*'''Tanya''': Week beginning 9th February<br />
*'''MariaC''': Week beginning 16th February<br />
*'''Rachael(UCL)''': Week beginning 23rd February<br />
*'''Kimberly''': Week beginning 2nd March<br />
*'''Rama''': Week beginning 9th March<br />
*'''David OS''': Week beginning 16th March<br />
*'''Moni''': Week beginning 23rd March<br />
*'''Harold''': Week beginning 30th March<br />
*'''Victoria(RGD)''': Week beginning 6th April<br />
*'''Petra(Dicty) ''': Week beginning 13th April<br />
*'''Tanya''': Week beginning 20th April<br />
*'''Rama''': Week beginning 27th April<br />
<br />
Victoria, Petra, Helen(Fly), Rachael, Becky have offered to be on the rotation 2x a year.<br />
<br><br />
<br />
At the end of your shift, please send a reminder email to the next person on the list to remind them that it's their turn. Thanks.<br />
<br />
[[Gohelp|GO help main page]]<br />
<br />
The software rota is concurrent with the main rota:<br />
<br />
[[Gohelp_software_rota]]<br />
<br />
[[JIRA issues|GO-Help JIRA issues]]</div>Mariahttps://wiki.geneontology.org/index.php?title=2013_Cambridge_Logistics&diff=438552013 Cambridge Logistics2013-02-04T14:46:59Z<p>Maria: /* Attendees */</p>
<hr />
<div>=Dates=<br />
<br />
The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following [http://www.ebi.ac.uk/biocuration2013/home Biocuration 2013].<br />
<br />
=Agendas=<br />
<br />
* [[2013 Cambridge GOC Meeting Agenda]]<br />
* [[2013 Cambridge GO SAB Meeting Agenda]]<br />
<br />
=Venue=<br />
<br />
The meeting will be held in the [http://www.mollercentre.co.uk/index.html Moller Centre], Churchill College, Cambridge.<br />
<br />
==Restaurants==<br />
<br />
There will be a group dinner on Thursday 11th April at the Moller Centre.<br />
<br />
Other evenings you will be on your own.<br />
<br />
Some suggestions of restaurants reasonably close to the Moller Centre:<br />
<br />
[http://www.cafenaz.co.uk/cambridge.php?id=7 Cafe Naz (Indian)]<br />
<br />
[http://www.restaurant-guide.com/maharajah.htm The Maharajah (Indian)]<br />
<br />
[http://www.cambscuisine.com/st-johns-chop-house/ St. John's Chop House (British)]<br />
<br />
[http://www.lamargheritacambridge.com/index.php La Margherita (Italian)]<br />
<br />
[http://www.prezzorestaurants.co.uk/restaurant/cambridge Prezzo (Italian)]<br />
<br />
[http://www.yippeenoodlebar.co.uk/ Yippee Noodle Bar (Asian)]<br />
<br />
[http://www.restaurant-guide.com/the-river-bar-steakhouse-and-grill.htm The River Bar (Steakhouse and Grill)]<br />
<br />
<br />
You will pass numerous pubs as you walk into Cambridge, some of which serve food, and plenty of other restaurants/cafes in the centre.<br />
<br />
Pubs:<br />
<br />
[http://thecastleinncambridge.com/ The Castle]<br />
<br />
[http://www.taylor-walker.co.uk/pub/pickerel-cambridge/c3602/ The Pickerel]<br />
<br />
[http://www.maypolefreehouse.co.uk/Welcome.html The Maypole]<br />
<br />
[http://gkpubs.co.uk/pubs-in-cambridge/eagle-pub/ The Eagle]<br />
<br />
The SAB dinner for PIs and SAB members will be on Friday 12th April<br />
<br />
==Weather==<br />
<br />
Cool, spring-like. <br />
<br />
==Maps==<br />
<br />
[http://map.cam.ac.uk/Churchill+College Interactive map of Cambridge]<br />
<br />
==Local activities==<br />
<br />
[http://cambridgesciencefestival.org/2013Festival/2013Festival.aspx Cambridge Science Festival] April 12-21st<br />
<br />
[http://www.kettlesyard.co.uk Kettles Yard Museum and House] - The gallery and house are well worth a visit and are just a short walk from the Moller Centre.<br />
<br />
[http://www.cam.ac.uk/museums/ Cambridge museums]<br />
<br />
Hopefully there will be some spring flowers along 'The Backs' down Queen's Road behind King's College.<br />
<br />
=Registration=<br />
<br />
Registration fees and a link to register for the meeting and book your accommodation will follow.<br />
<br />
Please indicate if you will be attending this meeting (on site or remotely) in the table below. <br />
We will provide toll free telephone & conferencing for remote attendees. <br />
<br />
==Remote Attendees==<br />
We will use the GO conference line. <br><br />
Toll-free USA number 1-866-953-9688 (US Toll number 1-212-548-2460 in case of problems with 866 number)<br><br />
Toll-free UK 0808 238 6001 (toll number: 646 834-9311)<br><br />
Toll-free Switzerland 0800 562 830 (toll number: 646 834-9311)<br><br />
<br />
Participant Pin: (801-561)<br><br />
<br />
=Lodging Information=<br />
<br />
Rooms have been reserved in [http://www.churchillconferences.co.uk/accommodation.php Churchill College] from 10-13th April.<br />
<br />
Breakfast is included.<br />
<br />
'''Booking'''<br />
<br />
Please indicate which nights you would like accommodation in the 'Attendees' table at the bottom of this page. You will be able to book your accommodation from the registration link as soon as it is available.<br />
<br />
N.B. If you are attending the Biocuration meeting before this meeting and would like to stay in the same room, please indicate 'Y' in the 'Extend room reservation from Biocuration meeting?' column.<br />
<br />
==Airports==<br />
<br />
[http://www.heathrowairport.com Heathrow Airport]<br />
<br />
[http://www.stanstedairport.com Stansted]<br />
<br />
[http://www.londoncityairport.com London City]<br />
<br />
==Ground transportation== <br />
<br />
[http://www.nationalrail.co.uk Train Information]<br />
<br />
[http://www.nationalexpress.com National Express coaches]<br />
<br />
[http://www.chu.cam.ac.uk/visitors/directions/ Driving directions] to the Moller Centre. For those driving, the Moller Centre has free parking.<br />
<br />
[http://www.theaa.com/route-planner/index.jsp AA Route planner]<br />
<br />
===Taxi Companies===<br />
<br />
Panther Taxis <br />
Website: www.panthertaxis.co.uk <br />
Tel: +44 (0)1223 715715<br />
<br />
Sawston Cab Co Ltd (Airport Specialist) <br />
Email: info@sawstoncabcoltd.co.uk <br />
Tel: +44 (0)1223 517008<br />
<br />
==Contacts==<br />
<br />
Rachael Huntley (huntley@ebi.ac.uk)<br />
<br />
Amy Cottage (cottage@ebi.ac.uk)<br />
<br />
=Attendees=<br />
<br />
'''Please note: if you are attending the Biocuration meeting before this meeting and would like to stay in the same room, please indicate 'Y' in the 'Extend room reservation from Biocuration meeting?' column.<br />
'''<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Nights required for accommodation (10,11,12,13 Apr?)<br />
! Extend room reservation from Biocuration meeting?<br />
! Remote attendee? (Y/N)<br />
! Attending Thursday dinner? (venue tbc)<br />
! Dietary requirements<br />
|-<br />
|Rachael Huntley<br />
|UniProt-GOA<br />
|N/A<br />
|N/A<br />
|N<br />
|Y<br />
|Lacto-ovo vegetarian<br />
|-<br />
|Mike Cherry<br />
|Stanford University<br />
|N/A<br />
|N/A<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Ruth Lovering<br />
|BHF-UCL<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Stacia Engel<br />
|Stanford University<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Edith Wong<br />
|Stanford University<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Val Wood<br />
|PomBase (Cambridge University)<br />
|n/a<br />
|N<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Petra Fey<br />
|dictyBase (Northwestern University)<br />
|Wed 10, Thu 11, Fri 12<br />
|Y<br />
|N<br />
|Y<br />
|no red meat<br />
|-<br />
|Venkat Malladi<br />
|Stanford University<br />
|Wed 10, Thu 11, Fri 12<br />
|Y<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|-<br />
|Maria Costanzo<br />
|Stanford University<br />
|Wed 10, Thu 11, Fri 12<br />
|Y<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Susan Tweedie<br />
|FlyBase (University of Cambridge)<br />
|n/a<br />
|n/a<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Prudence Mutowo<br />
|UniProt-GOA<br />
|n/a<br />
|n/a<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Tony Sawford<br />
|UniProt-GOA<br />
|n/a<br />
|n/a<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Jane Lomax<br />
|EBI-GO<br />
|N/A<br />
|N/A<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|}</div>Mariahttps://wiki.geneontology.org/index.php?title=2013_Cambridge_Logistics&diff=438482013 Cambridge Logistics2013-02-03T15:55:59Z<p>Maria: /* Attendees */</p>
<hr />
<div>=Dates=<br />
<br />
The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following [http://www.ebi.ac.uk/biocuration2013/home Biocuration 2013].<br />
<br />
=Agendas=<br />
<br />
* [[2013 Cambridge GOC Meeting Agenda]]<br />
* [[2013 Cambridge GO SAB Meeting Agenda]]<br />
<br />
=Venue=<br />
<br />
The meeting will be held in the [http://www.mollercentre.co.uk/index.html Moller Centre], Churchill College, Cambridge.<br />
<br />
==Restaurants==<br />
<br />
There will be a group dinner on Thursday 11th April at the Moller Centre.<br />
<br />
Other evenings you will be on your own.<br />
<br />
Some suggestions of restaurants reasonably close to the Moller Centre:<br />
<br />
[http://www.cafenaz.co.uk/cambridge.php?id=7 Cafe Naz (Indian)]<br />
<br />
[http://www.restaurant-guide.com/maharajah.htm The Maharajah (Indian)]<br />
<br />
[http://www.cambscuisine.com/st-johns-chop-house/ St. John's Chop House (British)]<br />
<br />
[http://www.lamargheritacambridge.com/index.php La Margherita (Italian)]<br />
<br />
[http://www.prezzorestaurants.co.uk/restaurant/cambridge Prezzo (Italian)]<br />
<br />
[http://www.yippeenoodlebar.co.uk/ Yippee Noodle Bar (Asian)]<br />
<br />
[http://www.restaurant-guide.com/the-river-bar-steakhouse-and-grill.htm The River Bar (Steakhouse and Grill)]<br />
<br />
<br />
You will pass numerous pubs as you walk into Cambridge, some of which serve food, and plenty of other restaurants/cafes in the centre.<br />
<br />
Pubs:<br />
<br />
[http://thecastleinncambridge.com/ The Castle]<br />
<br />
[http://www.taylor-walker.co.uk/pub/pickerel-cambridge/c3602/ The Pickerel]<br />
<br />
[http://www.maypolefreehouse.co.uk/Welcome.html The Maypole]<br />
<br />
[http://gkpubs.co.uk/pubs-in-cambridge/eagle-pub/ The Eagle]<br />
<br />
The SAB dinner for PIs and SAB members will be on Friday 12th April<br />
<br />
==Weather==<br />
<br />
Cool, spring-like. <br />
<br />
==Maps==<br />
<br />
[http://map.cam.ac.uk/Churchill+College Interactive map of Cambridge]<br />
<br />
==Local activities==<br />
<br />
[http://cambridgesciencefestival.org/2013Festival/2013Festival.aspx Cambridge Science Festival] April 12-21st<br />
<br />
[http://www.kettlesyard.co.uk Kettles Yard Museum and House] - The gallery and house are well worth a visit and are just a short walk from the Moller Centre.<br />
<br />
[http://www.cam.ac.uk/museums/ Cambridge museums]<br />
<br />
Hopefully there will be some spring flowers along 'The Backs' down Queen's Road behind King's College.<br />
<br />
=Registration=<br />
<br />
Registration fees and a link to register for the meeting and book your accommodation will follow.<br />
<br />
Please indicate if you will be attending this meeting (on site or remotely) in the table below. <br />
We will provide toll free telephone & conferencing for remote attendees. <br />
<br />
==Remote Attendees==<br />
We will use the GO conference line. <br><br />
Toll-free USA number 1-866-953-9688 (US Toll number 1-212-548-2460 in case of problems with 866 number)<br><br />
Toll-free UK 0808 238 6001 (toll number: 646 834-9311)<br><br />
Toll-free Switzerland 0800 562 830 (toll number: 646 834-9311)<br><br />
<br />
Participant Pin: (801-561)<br><br />
<br />
=Lodging Information=<br />
<br />
Rooms have been reserved in [http://www.churchillconferences.co.uk/accommodation.php Churchill College] from 10-13th April.<br />
<br />
Breakfast is included.<br />
<br />
'''Booking'''<br />
<br />
Please indicate which nights you would like accommodation in the 'Attendees' table at the bottom of this page. You will be able to book your accommodation from the registration link as soon as it is available.<br />
<br />
N.B. If you are attending the Biocuration meeting before this meeting and would like to stay in the same room, please indicate 'Y' in the 'Extend room reservation from Biocuration meeting?' column.<br />
<br />
==Airports==<br />
<br />
[http://www.heathrowairport.com Heathrow Airport]<br />
<br />
[http://www.stanstedairport.com Stansted]<br />
<br />
[http://www.londoncityairport.com London City]<br />
<br />
==Ground transportation== <br />
<br />
[http://www.nationalrail.co.uk Train Information]<br />
<br />
[http://www.nationalexpress.com National Express coaches]<br />
<br />
[http://www.chu.cam.ac.uk/visitors/directions/ Driving directions] to the Moller Centre. For those driving, the Moller Centre has free parking.<br />
<br />
[http://www.theaa.com/route-planner/index.jsp AA Route planner]<br />
<br />
===Taxi Companies===<br />
<br />
Panther Taxis <br />
Website: www.panthertaxis.co.uk <br />
Tel: +44 (0)1223 715715<br />
<br />
Sawston Cab Co Ltd (Airport Specialist) <br />
Email: info@sawstoncabcoltd.co.uk <br />
Tel: +44 (0)1223 517008<br />
<br />
==Contacts==<br />
<br />
Rachael Huntley (huntley@ebi.ac.uk)<br />
<br />
Amy Cottage (cottage@ebi.ac.uk)<br />
<br />
=Attendees=<br />
<br />
'''Please note: if you are attending the Biocuration meeting before this meeting and would like to stay in the same room, please indicate 'Y' in the 'Extend room reservation from Biocuration meeting?' column.<br />
'''<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Nights required for accommodation (10,11,12,13 Apr?)<br />
! Extend room reservation from Biocuration meeting?<br />
! Remote attendee? (Y/N)<br />
! Attending Thursday dinner? (venue tbc)<br />
! Dietary requirements<br />
|-<br />
|Rachael Huntley<br />
|UniProt-GOA<br />
|N/A<br />
|N/A<br />
|N<br />
|Y<br />
|Lacto-ovo vegetarian<br />
|-<br />
|Mike Cherry<br />
|Stanford University<br />
|N/A<br />
|N/A<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Ruth Lovering<br />
|BHF-UCL<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Stacia Engel<br />
|Stanford University<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Edith Wong<br />
|Stanford University<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Val Wood<br />
|PomBase (Cambridge University)<br />
|n/a<br />
|N<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Petra Fey<br />
|dictyBase (Northwestern University)<br />
|Wed 10, Thu 11, Fri 12<br />
|Y<br />
|N<br />
|Y<br />
|no red meat<br />
|-<br />
|Venkat Malladi<br />
|Stanford University<br />
|Wed 10, Thu 11, Fri 12<br />
|Y<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|-<br />
|Maria Costanzo<br />
|Stanford University<br />
|Wed 10, Thu 11, Fri 12 (possibly also 13th - will update)<br />
|Y<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|}</div>Mariahttps://wiki.geneontology.org/index.php?title=User_Advocacy&diff=38156User Advocacy2011-11-14T16:27:35Z<p>Maria: </p>
<hr />
<div>The purpose of the User Advocacy group is to establish lines of communication between the scientific community and the GO Consortium. The goal is to ensure that the GOC does not become insular and remains receptive to the needs of the scientific community. In addition, open lines of communication will increase the awareness and usefulness of GO in the scientific community.<br />
<br />
This purpose includes:<br />
#ensuring that changes in the GO are publicized and communicated to the community<br />
#acting as a broker between the community and the GOC so that the GOC does not become insular<br />
#providing user support for the products produced by GO<br />
#providing documentation for the products produced by GO.<br />
<br />
This group will ensure that GO remains useful, relevant, and accessible to the scientific community. This [[Media:Advocacy_diagram_v4.jpg|figure]] outlines this group's aims and organisation.<br />
<br />
==Sections:==<br />
<br />
*[[gohelp|GO helpdesk]]<br />
*[[news feed|News pages]]<br />
*[[Annotation_Outreach_group_reports|Monthly Reports]]<br />
<br />
'''Overview:'''<br />
*[[User Advocacy group summary]]<br />
*[[Media:Advocacy_diagram_v4.jpg|User Advocacy group figure]] ([[Media:TasksSimple.jpg|GOC-2007]])<br />
*[[User Advocacy group aims 2006]]<br />
*[http://www.valleypistachio.com/ dried fruit]<br />
<br />
'''Working Groups:'''<br />
*[[:Category:Web_presence_working_group|Web presence working group]]<br />
*[[AmiGO_Hub|AmiGO Hub]]<br />
*[[News group]]<br />
<br />
'''Other:'''<br />
*[[newsletter]] - discontinued as of Oct 2008. See [[news feed]].<br />
*[[GO survey 2009/10]]<br />
*[[users_meetings|Future Users Meetings]]<br />
*[[tools_standards|Standards for GO tools]]<br />
*[[journals_advice|RSC journals: marking up text]]<br />
*[[Documentation needed]]<br />
*[[Future outreach/advocacy at specific meetings]]<br />
<br />
<br />
[[Outreach and Advocacy]]<br />
<br />
[[Individual Meeting Plans]]<br />
<br />
[[Category:Advocacy and Outreach]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Main_Page&diff=38154Main Page2011-11-12T20:06:25Z<p>Maria: </p>
<hr />
<div><big>'''Welcome to the Gene Ontology Consortium Wiki'''</big><br />
<br />
== GOC Public Resources ==<br />
<br />
[[:Category:FAQ|GO Frequently Asked Questions]]<br />
<br />
=== Community Annotation Pages ===<br />
[[Cardiovascular|Cardiovascular Genes]]<br />
<br />
[[Immunology]]<br />
<br />
[[Lung Development]]<br />
<br />
[[Muscle Biology|Muscle Biology]]<br />
<br />
[[Reference Genome Genes]]<br />
<br />
=== Web Pages ===<br />
<br />
* [http://www.geneontology.org/ GO Home]<br />
* [http://www.geneontology.org/GO.contents.doc.shtml GO Documentation]<br />
* [http://www.geneontology.org/GO.downloads.shtml GO Downloads]<br />
<br />
=== Database Query Pages ===<br />
* [http://amigo.geneontology.org AmiGO]<br />
<br />
== GO Working Group Wiki ==<br />
<br />
These pages are limited to use by members of the GOC.<br />
<br />
*[[User Advocacy]]<br />
*[[Annotation Outreach]]<br />
*[[Ontology Development]]<br />
*[[Reference Genome Annotation Project]]<br />
*[[Software and Utilities]]<br />
<br />
*[[GO Leadership]]<br />
*[[GO Managers]]<br />
*[[Consortium Meetings]]<br />
*[[Working Groups]]<br />
**[[AmiGO Hub]] <span class="plainlinks">[http://www.valleypistachio.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">dried fruit</span>]<br />
**[[:Category:OBO-Edit working group|OBO-Edit working group]]<br />
**[[:Category:Web Presence Working Group|Web Presence Working Group]]<br />
**[[:Category:Immunology Annotation working group|Immunology Annotation working group]]<br />
**[[Web Presence Working Group]]<br />
*[[GO Content Checklist]]<br />
*[[Progress Reports]] <span class="plainlinks">[http://www.netlook.com.br/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">roupas da moda</span>]<br />
*[[Publications%2C_tutorials%2C_talks%2C_posters|Publication list]]<br />
<br />
== Useful Links ==<br />
<br />
Help pages for using wikis: http://meta.wikimedia.org/wiki/Help:Help<br />
<br />
Quick guide to formatting wiki text: http://meta.wikimedia.org/wiki/Help:Wikitext<br />
<br />
[[Wiki_best_practice|Guidelines for using this wiki]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Main_Page&diff=38153Main Page2011-11-12T20:05:08Z<p>Maria: </p>
<hr />
<div><big>'''Welcome to the Gene Ontology Consortium Wiki'''</big><br />
<br />
== GOC Public Resources ==<br />
<br />
[[:Category:FAQ|GO Frequently Asked Questions]]<br />
<br />
=== Community Annotation Pages ===<br />
[[Cardiovascular|Cardiovascular Genes]]<br />
<br />
[[Immunology]]<br />
<br />
[[Lung Development]]<br />
<br />
[[Muscle Biology|Muscle Biology]]<br />
<br />
[[Reference Genome Genes]]<br />
<br />
=== Web Pages ===<br />
<br />
* [http://www.geneontology.org/ GO Home]<br />
* [http://www.geneontology.org/GO.contents.doc.shtml GO Documentation]<br />
* [http://www.geneontology.org/GO.downloads.shtml GO Downloads]<br />
<br />
=== Database Query Pages ===<br />
* [http://amigo.geneontology.org AmiGO]<br />
<br />
== GO Working Group Wiki ==<br />
<br />
These pages are limited to use by members of the GOC.<br />
<br />
*[[User Advocacy]]<br />
*[[Annotation Outreach]]<br />
*[[Ontology Development]]<br />
*[[Reference Genome Annotation Project]]<br />
*[[Software and Utilities]]<br />
<br />
*[[GO Leadership]]<br />
*[[GO Managers]]<br />
*[[Consortium Meetings]]<br />
*[[Working Groups]]<br />
**[[AmiGO Hub]] <span class="plainlinks">[http://www.valleypistachio.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">dried fruitr</span>]<br />
**[[:Category:OBO-Edit working group|OBO-Edit working group]]<br />
**[[:Category:Web Presence Working Group|Web Presence Working Group]]<br />
**[[:Category:Immunology Annotation working group|Immunology Annotation working group]]<br />
**[[Web Presence Working Group]]<br />
*[[GO Content Checklist]]<br />
*[[Progress Reports]] <span class="plainlinks">[http://www.netlook.com.br/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">roupas da moda</span>]<br />
*[[Publications%2C_tutorials%2C_talks%2C_posters|Publication list]]<br />
<br />
== Useful Links ==<br />
<br />
Help pages for using wikis: http://meta.wikimedia.org/wiki/Help:Help<br />
<br />
Quick guide to formatting wiki text: http://meta.wikimedia.org/wiki/Help:Wikitext<br />
<br />
[[Wiki_best_practice|Guidelines for using this wiki]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Ontology_Development&diff=38067Ontology Development2011-11-06T15:11:59Z<p>Maria: /* Proposed content work */</p>
<hr />
<div>This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes <span class="plainlinks">[http://thebeginnerslens.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">iphone photography</span>] and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions <span class="plainlinks">[http://www.bestpills4weightloss.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">weight loss pills</span>] to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.<br />
<br />
==Content Development ==<br />
===Priority ranking===<br />
====High Priority====<br />
*Cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]<br />
**[[Cell cross-products]] (Jane, Alex, Chris, others?)<br />
**[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, Harold, Midori)<br />
*[[Function-Process Links]]<br />
*[[Chemical terms in GO]](Part of the CHEbi alignment process)<br />
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David)<br />
*[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)<br />
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts)<br />
<br />
====Medium Priority====<br />
*[[Non-symbiotic multi-organism processes]]<br />
*[[Neurobiology Project]] (David, Tanya, Jane, Paola)<br />
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)<br />
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)<br />
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)<br />
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)<br />
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris)<br />
<br />
====Low priority====<br />
*Peripheral nervous system development<br />
*[[Uberon alignment]]<br />
<br />
===Timeline===<br />
<br />
[[2010 Timeline]]<br />
<br />
[[2011 Timeline]]<br />
<br />
[[2012 Timeline]]<br />
<br />
===Proposed content work===<br />
A list of topics that <span class="plainlinks">[https://www.proposable.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">proposal software</span>] we propose to address, but for which a timeline has not been set<br />
<br />
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology. <br />
*Rework disjoint terms as [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list].<br />
*Overhaul [[translation]], similar to what's being done for transcription. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)<br />
* [[Recombination and DNA repair]]<br />
* [[RNA processes]]<br />
* cell cycle<br />
* [[Bile formation and secretion processes]]<br />
* [[multi-organism processes v/s cellular processes]]<br />
* [[protein and peptidyl amino acid modification / protein processing]]<br />
* [[Response to drug]]<br />
* [[Polyketide synthases]]<br />
* [[cell growth/proliferation/division]]<br />
* [[oxidoreductases]]<br />
<br />
===[[Completed ontology content work]]===<br />
<br />
==Other Ontology Development Group Activities==<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*[[Tracker wishlist]]<br />
*[[Content Meeting Documentation]]<br />
**[http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information|Content meeting participants' information]<br />
*[[:Category:Curator Guides|Curator guides]]<br />
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation<br />
*[[microbial ontology development and annotation]]<br />
*[[New Ontology Editor Training]]<br />
*[[Cell-type specific GO terms]]<br />
*[[Ontology_Development_Reports|Reports]]<br />
<br />
==Editor's Conference calls-weekly 7-7.30 AM PST==<br />
*[[July 6]]<br />
*[[July 20]]<br />
*[[Aug 3]]<br />
*[[Aug 17]]<br />
*[[Aug 31]]<br />
*[[Ontology meeting 2011-09-14|Sept 14]]<br />
*[[Ontology meeting 2011-09-28|Sept 28]]<br />
*[[Ontology meeting 2011-10-05|Oct 5]]<br />
*[[Ontology meeting 2011-10-12|Oct 12]]<br />
*[[Ontology meeting 2011-10-19|Oct 19]]<br />
*[[Ontology meeting 2011-10-26|Oct 26]]<br />
*[[Ontology meeting 2011-11-02|Nov 2]]<br />
*[[Ontology meeting 2011-11-16|Nov 16]]<br />
*[[Ontology meeting 2011-11-23|Nov 23]]<br />
*[[Ontology meeting 2011-11-30|Nov 30]]<br />
*[[Ontology meeting 2011-12-7|Dec 7]]<br />
*[[Ontology meeting 2011-12-14|Dec 14]]<br />
*[[Ontology meeting 2011-12-21|Dec 21]]<br />
<br />
==Administrative==<br />
*[[Ontology Development group summary]]<br />
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]<br />
<br />
[[Category:Ontology]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Ontology_Development&diff=37763Ontology Development2011-10-28T13:36:09Z<p>Maria: </p>
<hr />
<div>This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes <span class="plainlinks">[http://thebeginnerslens.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">iphone photography</span>] and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions <span class="plainlinks">[http://www.bestpills4weightloss.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">weight loss pills</span>] to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.<br />
<br />
==Content Development ==<br />
===Priority ranking===<br />
====High Priority====<br />
*Cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]<br />
**[[Cell cross-products]] (Jane, Alex, Chris, others?)<br />
**[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, Harold, Midori)<br />
*[[Function-Process Links]]<br />
*[[Chemical terms in GO]](Part of the CHEbi alignment process)<br />
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David)<br />
*[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)<br />
*[[Apoptosis]]<br />
<br />
====Medium Priority====<br />
*[[Non-symbiotic multi-organism processes]]<br />
*[[Neurobiology Project]] (David, Tanya, Jane, Paola)<br />
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)<br />
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)<br />
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)<br />
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)<br />
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris)<br />
<br />
====Low priority====<br />
*Peripheral nervous system development<br />
*[[Uberon alignment]]<br />
<br />
===Timeline===<br />
<br />
[[2010 Timeline]]<br />
<br />
[[2011 Timeline]]<br />
<br />
===Proposed content work===<br />
A list of topics that we propose to address, but for which a timeline has not been set<br />
<br />
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology. <br />
*Rework disjoint terms as [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list].<br />
*Overhaul [[translation]], similar to what's being done for transcription. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)<br />
* [[Recombination and DNA repair]]<br />
* [[RNA processes]]<br />
* [[Bile formation and secretion processes]]<br />
* [[multi-organism processes v/s cellular processes]]<br />
* [[protein and peptidyl amino acid modification / protein processing]]<br />
* [[Response to drug]]<br />
* [[Polyketide synthases]]<br />
* [[cell growth/proliferation/division]]<br />
* [[oxidoreductases]]<br />
<br />
===[[Completed ontology content work]]===<br />
<br />
==Other Ontology Development Group Activities==<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*[[Tracker wishlist]]<br />
*[[Content Meeting Documentation]]<br />
**[http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information|Content meeting participants' information]<br />
*[[:Category:Curator Guides|Curator guides]]<br />
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation<br />
*[[microbial ontology development and annotation]]<br />
*[[New Ontology Editor Training]]<br />
*[[Cell-type specific GO terms]]<br />
*[[Ontology_Development_Reports|Reports]]<br />
<br />
==Editor's Conference calls-weekly 7-7.30 AM PST==<br />
*[[July 6]]<br />
*[[July 20]]<br />
*[[Aug 3]]<br />
*[[Aug 17]]<br />
*[[Aug 31]]<br />
*[[Ontology meeting 2011-09-14|Sept 14]]<br />
*[[Ontology meeting 2011-09-28|Sept 28]]<br />
*[[Ontology meeting 2011-10-05|Oct 5]]<br />
*[[Ontology meeting 2011-10-12|Oct 12]]<br />
*[[Ontology meeting 2011-10-19|Oct 19]]<br />
*[[Ontology meeting 2011-10-26|Oct 26]]<br />
*[[Ontology meeting 2011-11-02|Nov 2]]<br />
*[[Ontology meeting 2011-11-16|Nov 16]]<br />
*[[Ontology meeting 2011-11-23|Nov 23]]<br />
*[[Ontology meeting 2011-11-30|Nov 30]]<br />
*[[Ontology meeting 2011-12-7|Dec 7]]<br />
*[[Ontology meeting 2011-12-14|Dec 14]]<br />
*[[Ontology meeting 2011-12-21|Dec 21]]<br />
<br />
==Administrative==<br />
*[[Ontology Development group summary]]<br />
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]<br />
<br />
[[Category:Ontology]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Main_Page&diff=37761Main Page2011-10-28T13:27:01Z<p>Maria: /* GO Working Group Wiki */</p>
<hr />
<div><big>'''Welcome to the Gene Ontology Consortium Wiki'''</big><br />
<br />
== GOC Public Resources ==<br />
<br />
[[:Category:FAQ|GO Frequently Asked Questions]]<br />
<br />
=== Community Annotation Pages ===<br />
[[Cardiovascular|Cardiovascular Genes]]<br />
<br />
[[Immunology]]<br />
<br />
[[Muscle Biology|Muscle Biology]]<br />
<br />
[[Reference Genome Genes]]<br />
<br />
[[Lung Development]]<br />
<br />
=== Web Pages ===<br />
<br />
* [http://www.geneontology.org/ GO Home]<br />
* [http://www.geneontology.org/GO.contents.doc.shtml GO Documentation]<br />
* [http://www.geneontology.org/GO.downloads.shtml GO Downloads]<br />
<br />
=== Database Query Pages ===<br />
* [http://amigo.geneontology.org AmiGO]<br />
<br />
== GO Working Group Wiki ==<br />
<br />
These pages are limited to use by members of the GOC.<br />
<br />
*[[User Advocacy]]<br />
*[[Annotation Outreach]]<br />
*[[Ontology Development]]<br />
*[[Reference Genome Annotation Project]]<br />
*[[Software and Utilities]]<br />
*<span class="plainlinks">[http://www.bestpills4weightloss.com/ <span style="color:blue;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">weight loss pills</span>]<br />
*[[GO Leadership]]<br />
*[[GO Managers]]<br />
*<span class="plainlinks">[http://thebeginnerslens.com/ <span style="color:blue;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">iphone photography</span>]<br />
*[[Consortium Meetings]]<br />
*[[Working Groups]]<br />
**[[AmiGO Hub]]<br />
**[[:Category:OBO-Edit working group|OBO-Edit working group]]<br />
**[[:Category:Web Presence Working Group|Web Presence Working Group]]<br />
**[[:Category:Immunology Annotation working group|Immunology Annotation working group]]<br />
**[[Web Presence Working Group]]<br />
*[[GO Content Checklist]]<br />
*[[Progress Reports]]<br />
*[[Publications%2C_tutorials%2C_talks%2C_posters|Publication list]]<br />
<br />
== Useful Links ==<br />
<br />
Help pages for using wikis: http://meta.wikimedia.org/wiki/Help:Help<br />
<br />
Quick guide to formatting wiki text: http://meta.wikimedia.org/wiki/Help:Wikitext<br />
<br />
[[Wiki_best_practice|Guidelines for using this wiki]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Annotation&diff=37304Annotation2011-09-26T03:08:18Z<p>Maria: </p>
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<hr />
<div>=Dates=<br />
The GO meeting will be begin at 9am on May 19, 2011 and end at 1pm on May 21, 2011, and will be held at the University of Southern California in Los Angeles.<br />
<br />
=Venue=<br />
Cardinal and Gold Room<br/><br />
Davidson Conference Center ([http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=3415+South+Figueroa+Street,+Los+Angeles,+CA&aq=0&sll=37.0625,-95.677068&sspn=38.690438,61.435547&ie=UTF8&hq=&hnear=3415+S+Figueroa+St,+Los+Angeles,+California+90007&z=16 map])<br/><br />
University of Southern California<br/><br />
3415 South Figueroa Street<br/><br />
Los Angeles, CA 90089-0871<br />
<br />
=Registration=<br />
Register by entering your name in the Attendees section below.<br />
<br />
*There will be a registration fee of $120 to cover the breakfasts, lunches and coffee breaks. This will be payable by credit card the first day of the meeting.<br />
<br />
=Lodging Information=<br />
Hotel confirmation numbers are in the Attendee table below, for everyone who registered prior to May 1. We are no longer arranging for hotel, so if you register after May 1, please arrange for your own hotel. The JW Marriott below still has availability as of May 1.<br />
<br />
Downtown is only a 10 min. ride away (we will arrange for shuttle service and there is also fast, cheap local transportation on the DASH). If you want to share a room, please contact Pauline Martinez at pauline.martinez@med.usc.edu.<br />
<br />
----<br />
Downtown:<br/><br />
[http://www.marriott.com/hotels/travel/laxjw-jw-marriott-hotel-los-angeles-at-la-live/ JW Marriott Los Angeles L.A. LIVE]<br/><br />
900 West Olympic Boulevard, Los Angeles, CA 90015<br/><br />
----<br />
Campus:<br/><br />
'''NOTE: THIS HOTEL IS NOW FULL (AS OF APRIL 19), PLEASE USE DOWNTOWN OPTION'''<br/><br />
[http://www.radisson.com/los-angeles-hotel-ca-90007/cafiguer Radisson Los Angeles at USC]<br/><br />
3540 S. Figueroa Street, Los Angeles, CA 90007<br/><br />
----<br />
<br />
=Maps and Transportation=<br />
==Airport to Hotel==<br />
* LA taxis have a flat rate to downtown (not the USC campus) of $46.50 (not including tip)<br />
* Prime Time Shuttle<br />
** phone 1(800) 733-8267<br />
** USC rate to any USC location, including downtown: $13.50 per person<br />
==Downtown Hotel to USC Campus==<br />
* '''The [http://www.ladottransit.com/dash/routes/downtown/downtown.php DASH bus] ROUTE F, [http://www.ladottransit.com/dash/routes/downtown/downtown.pdf Map of DASH routes] runs every 10 min. on weekdays and costs 35 cents.'''<br />
* (Maybe a shuttle will arranged)<br />
<br />
=To do=<br />
Coming soon.<br />
<br />
=Meeting Agenda= <br />
<br />
The agenda can be found here: [[2011_USC_Meeting_Agenda]]<br />
<br />
=Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time from Airport <br />
! Departure Date/Time to Airport<br />
! Hotel pref. (Downtown/Campus) and confirmation<br />
! Vegetarian (Y/N)<br />
|-<br />
|Paul Thomas<br />
|USC/PANTHER/PortEco<br />
|N/A<br />
|N/A<br />
|Downtown<br />
|N<br />
|-<br />
| Paul Sternberg<br />
| Caltech/Wormbase<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Suzi Lewis<br />
| LBNL<br />
|<br />
|<br />
|Downtown Marriott JW Marriott/ Conf. #84481712<br />
|<br />
|-<br />
| Mike Cherry<br />
| Stanford/SGD<br />
| 1900 / May 18<br />
| 1500 / May 21<br />
| Downtown Marriott JW Marriott/ Conf. #84481712<br />
| N<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory/MGI<br />
| 1650 / May 18<br />
| 1110 / May 22<br />
| Downtown Marriott (5 nights) JW Marriott/ Conf. # 84974216<br />
| N<br />
|-<br />
| Rama Balakrishnan<br />
| SGD, Stanford University<br />
| May 18<br />
| May 21<br />
| Downtown Marriott JW Marriott/ Conf. #84481712<br />
| Y<br />
|-<br />
| Valerie Wood<br />
| PomBase, Cambridge University<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights) JW Marriott/ Conf. # 84974216<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN, U. Oregon<br />
| May 18 5:40PM<br />
| May 21<br />
| Campus (3 nights) RAD conf. #795754<br />
| N<br />
|-<br />
| David Hill<br />
| Jackson Laboratory/MGI<br />
| May 18th 1:36PM<br />
| May 21st 11:00PM<br />
| Campus RAD conf. #795744<br />
| N<br />
|-<br />
| Harold Drabkin<br />
| Jackson Laboratory/MGI/PRO<br />
| May 18 04:50 PM<br />
| May 21 3:00 PM<br />
| Campus (3 nights) RAD conf. #795751<br />
| N<br />
|-<br />
| Eurie Hong<br />
| Stanford/SGD<br />
| May 18<br />
| May 21<br />
| Downtown JW Marriott/ Conf. #84481712 (Dbl)<br />
| N<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| May 18<br />
| May 20<br />
| Campus (2 nights) RAD conf. #795752<br />
| N<br />
|-<br />
| Donghui Li<br />
| TAIR<br />
| May 18 16:25<br />
| May 21 14:55<br />
| Campus (3 nights) RAD conf. #795753<br />
| N<br />
|-<br />
| Eva Huala<br />
| TAIR<br />
| May 19 07:40<br />
| May 21 14:30<br />
| Campus (2 nights) RAD conf. # 814958<br />
| N<br />
|-<br />
| Susan Tweedie<br />
| FlyBase<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights) RAD conf. #795761<br />
| N<br />
|-<br />
| Julie Park<br />
| Stanford/SGD<br />
| May 18 <br />
| May 21 <br />
| Downtown<br />
| N<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| May 18<br />
| May 22<br />
| Campus (4 nights) RAD conf. #795760<br />
| N<br />
|-<br />
| Rebecca Foulger<br />
| GO-Editorial<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf. #795759<br />
| N<br />
|-<br />
| Paola Roncaglia<br />
| GO-Editorial<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf.#795758<br />
| N<br />
|-<br />
| Emily Dimmer<br />
| GOA<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf.#795757<br />
| N<br />
|-<br />
| Tony Sawford<br />
| GOA<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf. #795762<br />
| N<br />
|-<br />
| Claire O'Donovan<br />
| UniProt/GOA<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf. #795756<br />
| N (but coeliac)<br />
|-<br />
|Seth Carbon<br />
|BBOP<br />
|May 18<br />
|May 21<br />
|Downtown Marriott (3 nights) JW Marriott/ Conf. # 84455496<br />
|N<br />
|-<br />
| Marcus Chibucos<br />
| Institute for Genome Sciences/ECO<br />
| 18 May, 12:15 PM<br />
| 21 May, 10:35 PM<br />
| Campus (3 nights) RAD conf. #795755<br />
| Y (pescetarian)<br />
|-<br />
| Hans-Michael Muller<br />
| Textpresso / California Institute of Technology<br />
| N/A<br />
| N/A<br />
| N/A<br />
| N<br />
|-<br />
|Jim Hu<br />
|PortEco/EcoliWiki/Texas A&M<br />
|May 18<br />
|May 21<br />
|Downtown JW Marriott/ Conf. # 84455496<br />
|N (Lac<sup>-</sup>)<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|May 16, 9:00pm LAX<br />
|May 21, 10:00pm LAX<br />
|N/A<br />
|Y, please <br />
|-<br />
|Fiona McCarthy<br />
|AgBase<br />
|May 18 15:33, LAX<br />
|May 22 06:30, LAX<br />
|Downtown JW Marriott/ Conf. # 84455496<br />
|N <br />
|-<br />
| Ruth Lovering<br />
| BHF-UCL<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Downtown (4 nights) JW Marriott/ Conf. # 84455496<br />
| N<br />
|-<br />
| Sarah Burge<br />
| InterPro<br />
| May 18 13:40(ish)<br />
| May 22 17:45(ish)<br />
| Campus (4 nights: booked by EBI) RAD conf.#788405<br />
| Y<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| May 18 LAX 17:47<br />
| May 21 LAX 16:00 <br />
| Downtown (3 nights) JW Marriott/ Conf. # 84974216<br />
| Y<br />
|-<br />
| Heiko Dietze<br />
| LBNL<br />
| May 18 (5:25 Pm)<br />
| May 21 (5:20 Pm)<br />
| Downtown (3 nights) JW Marriott/ Conf. # 84972140<br />
| N<br />
|-<br />
| Amelia Ireland<br />
| BBOP<br />
| May 18 17:25<br />
| May 21 14:13<br />
| Downtown JW Marriott/ Conf. # 84972140<br />
| Y<br />
|-<br />
| Chris Mungall<br />
| BBOP<br />
| May 19 am<br />
| May 21 tbd<br />
| Downtown JW Marriott/ Conf. # 84972140<br />
| Y<br />
|-<br />
| Ranjana Kishore<br />
| WormBase/Caltech<br />
| N/A<br />
| N/A<br />
| N/A<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| dictyBase<br />
| May 18<br />
| May 21 LAX 11:50<br />
| <br />
| Y<br />
|-<br />
| Shahid Manzoor<br />
| LBNL<br />
| May 18 LAX<br />
| May 21 LAX 11:50<br />
| <br />
| Y<br />
|-<br />
|}<br />
<br />
=Remote Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
! Time Zone<br />
|-<br />
|Anushya Muruganujan<br />
|USC/PANTHER<br />
|muruganu@usc.edu<br />
|PDT<br />
|-<br />
|Peter D'Eustachio<br />
|NYU / Reactome<br />
|deustp01@nyumc.org<br />
|EDT<br />
|-<br />
|Mike Livstone (Friday only)<br />
|Princeton/P-POD<br />
|livstone@genomics.princeton.edu<br />
|EDT<br />
|-<br />
|Li NI<br />
|Jackson / MGI<br />
|ln@informatics.jax.org<br />
|EDT<br />
|-<br />
|Terry Meehan<br />
|Jackson / GOC /CL<br />
|tmeehan@informatics.jax.org<br />
|EDT<br />
|-<br />
|Mary Dolan<br />
|Jackson / MGI<br />
|mdolan@informatics.jax.org<br />
|EDT<br />
|-<br />
|Lakshmi Pillai<br />
|AgBase<br />
|laksrp@gmail.com<br />
|CDT<br />
|-<br />
|Cathy Gresham<br />
|AgBase<br />
|gresham@cse.msstate.edu<br />
|CDT<br />
|-<br />
|Trudy Torto-Alalibo<br />
|Microbial ENergy processes Gene Ontology (MENGO)VBI<br />
|trudy@vbi.vt.edu<br />
|EDT<br />
|-<br />
|Biswarup Mukhopadhyay<br />
|Microbial ENergy processes Gene Ontology (MENGO) VBI<br />
|biswarup@vt.edu<br />
|EDT<br />
|-<br />
|Karen Christie<br />
|Stanford/SGD<br />
|kchris@genome.stanford.edu<br />
|PDT<br />
|-<br />
|Pankaj Jaiswal<br />
|Oregon State/Gramene/PO<br />
|jaiswalp@science.oregonstate.edu<br />
|PDT<br />
|-<br />
|Alexander Diehl<br />
|SUNY Buffalo<br />
|addiehl@buffalo.edu<br />
|EDT<br />
|-<br />
|Brenley McIntosh<br />
|ProtEco/EcoliWiki/Texas A&M<br />
|brenleymcintosh@gmail.com<br />
|CDT<br />
|-<br />
|Daniel Renfro<br />
|PortEco/EcoliWiki/Texas A&M<br />
|bluecurio@gmail.com<br />
|CDT<br />
|-<br />
|Kim Rutherford<br />
|PomBase/University of Cambridge<br />
|kmr44@cam.ac.uk<br />
|BST<br />
|-<br />
|Varsha Khodiyar<br />
|BHF-UCL<br />
|vkhodiyar@ucl.ac.uk<br />
|BST<br />
|-<br />
|Sven Heinicke<br />
|Princeton<br />
|sven@genomics.princeton.edu<br />
|EDT<br />
|-<br />
|Dmitry Sitnikov<br />
|Jackson/MGI<br />
|dmitrys@informatics.jax.org<br />
|EDT<br />
|-<br />
|Maria Costanzo<br />
|Stanford<br />
|Maria.Costanzo@stanford.edu<br />
|EDT<br />
|}<br />
<br />
<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page<br />
[[Category:Meetings]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Sporulation_Meeting_Notes&diff=12202Sporulation Meeting Notes2008-04-02T14:41:36Z<p>Maria: /* April 2, 2008 Blastospores */</p>
<hr />
<div>==August 2007 - January 2008==<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
== Feb. 14, 2008 ==<br />
<br />
'''Midori''' (very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
:updated earlier draft; see Definitions below<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:''' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
==February 20, 2008 Skype "meeting"==<br />
Present: Midori, Debby, Maria, Pascale, Val<br />
<br />
===Meeting summary===<br />
(Midori)<br />
<br />
We discussed whether sporulation should go under reproduction; it's not resolved yet, but the other changes don't depend on the decision. If sporulation (GO:0030435) itself doesn't go under reproduction, descendants of sporulation can have reproduction as an additional parent as needed.<br />
<br />
Changes we did decide on:<br />
<br />
*Create two child terms, for spores produced by mitosis (= asexual) and by meiosis (sexual), The definitions probably need work; any other comments also welcome. Definitions below.<br />
*For types of sporulation observed in bacteria, Debby will look up distinguishing features that can be used in definitions; Midori will help convert that information into GO-definition-friendly sentences. See below ...<br />
*Rename 30437 to ascospore formation, and improve definition; also rename 30476 to ascospore wall assembly.<br />
*Move conidium formation (GO:0048315) to is_a mitotic/asexual sporulation. <br />
*We agreed to make three terms obsolete:<br />
**reproductive sporulation GO:0048622<br />
::This term is ill defined, so much so that we don't know what it was intended to mean; it also has a parent (reproductive process in single-celled organism) that isn't consistent with the 'sporulation whose primary biological objective is reproduction' meaning (true path violation - cf ferns, mosses, mushrooms). No gene products are annotated directly to GO:0048622<br />
:*sporulation (sensu Bacteria) GO:0030436<br />
::This is a grouping term that isn't useful -- there are several different types of spore formed by different species/genera/etc. of bacteria, and there is neither a need nor a good basis for grouping them with each other.<br />
:*spore wall assembly (sensu Bacteria) GO:0042243<br />
::Reasons analogous to those given for GO:0030436 above.<br />
<br />
<br />
'''Debby''' 2/20/08<br />
<br />
GO:0030435 sporulation<br />
<br />
*Sexual or meiotic spores (child term of sporulation) <br />
** Ascospores (meiotically produced spores form by Ascomycetes)<br />
** Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
** Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
** Ferns<br />
<br />
*Asexual or mitotic spores (child term of sporulation) <br />
**Arthrospores (aka oidia)(Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
**Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
**Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott) <br />
**Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes) <br />
**Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
**Dictyostelium - forms spores inside fruiting bodies<br />
**Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some low G+C Gram-positive bacteria)<br />
**Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.) <br />
**Myxospore<br />
**Actinomycetes (High G+C Gram-positive bacteria that form spores)<br />
<br />
'''Midori:''' Current draft of the proposed ontology structure (Feb. 20):<br />
<br />
sporulation GO:0030436<br><br />
[i] asexual sporulation GO:new<br><br />
--[i] conidium formation GO:0048315<br><br />
--[new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
[i] sexual sporulation GO:new<br />
--[i] ascospore formation GO:0030437 (renamed)<br><br />
-- --[p] ascospore wall formation GO:0030476 (renamed)<br><br />
-- --[p] ascospore-type prospore formation GO:0031321 (renamed; suggestions welcome for nicer new name)<br><br />
--[other new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
--[p] spore wall assembly GO:0042244<br><br />
-- --[i] ascospore wall formation GO:0030476 (renamed)<br><br />
-- --[other new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
<br />
===Definitions===<br />
(Feb. 26; Midori)<br />
(minor updates March 7; Midori)<br />
<br />
<pre><br />
id: GO:0030435<br />
name: sporulation<br />
def: "The process by which a relatively unspecialized cell acquires the specialized features <br />
of a spore, a cell form that can be used for dissemination, for survival of adverse conditions <br />
because of its heat and dessication resistance, and/or for reproduction.Spores are usually <br />
unicellular and may develop into vegetative organisms or gametes. They may be produced <br />
asexually or sexually and are of many types." [GOC:mah; ISBN:0072992913]<br />
<br />
id: GO:0030436<br />
name: asexual sporulation<br />
def: "The formation of spores derived from the products of mitosis." [GOC:mah; PMID: 9529886]<br />
synonym: "asexual spore formation" EXACT []<br />
synonym: "mitotic sporulation" EXACT []<br />
synonym: "mitotic spore formation" EXACT []<br />
synonym: "spore formation (sensu Bacteria)" NARROW []<br />
synonym: "sporulation (sensu Bacteria)" NARROW []<br />
is_a: GO:0030435 ! sporulation<br />
<br />
id: GO:new<br />
name: sexual sporulation<br />
def: "The formation of spores derived from the products of meiosis." [GOC:mah]<br />
synonym: "meiotic sporulation" EXACT []<br />
synonym: "meiotic spore formation" EXACT []<br />
synonym: "sexual spore formation" EXACT []<br />
is_a: GO:0030435 ! sporulation<br />
<br />
Note: any of the synonyms could be used as the term name, if you prefer.<br />
<br />
id: GO:0030437<br />
name: ascospore formation<br />
def: "The process by which a diploid cell undergoes meiosis, and the meiotic products <br />
acquire the specialized features of ascospores. Ascospores are generally found in clusters <br />
of four or eight spores within a single mother cell, the ascus, and are characteristic of the <br />
ascomycete fungi (phylum Ascomycota)." [GOC:mah; PMID:16339736]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
id: GO:new<br />
name: basidiospore formation<br />
def: "The process by which spores form outside a specialized end cell known as a basidium. <br />
Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to <br />
spores that each contain a haploid nucleus that is the product of meiosis. The spores are <br />
usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In <br />
most basidiomycetes there are four sterigmata (and four spores) to a basidium." [GOC:mah, <br />
GOC:ds, http://www.ilmyco.gen.chicago.il.us/Terms/basid133.html, <br />
http://www.gsbs.utmb.edu/microbook/ch073.htm]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
id: GO:new<br />
name: zygospore formation<br />
def: "The process by which zygospores are formed. Zygospores are characteristic of the <br />
zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily <br />
ornamented as well, with many spines or ridges. It is formed between two specialized organs <br />
called suspensors, which are themselves usually heavily ornamented, one from each mating <br />
partner. The zygospore forms between them and then breaks away." [GOC:mah, GOC:ds, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/zygos581.html]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
</pre><br />
<br />
more Feb. 28 (Midori)<br />
<br />
I think some of these are likely to require more work, because different sources don't quite agree on some things, especially for "chlamydospore" -- the Illinois Mycological Association fungal term glossary says that chlamydospores can be sexual or asexual. I'm also not sure where the part about hyphal fragmentation that Debby found in Prescott belongs. And we also have to deal with the existing term 'chlamydospore developmen GO:0001410, which is defined and used for structures in Candida that may not be true spores.<br />
<br />
I've concocted two possible versions, with one or two chlamydospore formation terms (note that neither option considers the GO:0001410 wrinkle).<br />
<br />
refs: PMID: 16215181, http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html, the wiki and sources noted therein<br />
<br />
<pre><br />
<br />
One possibility:<br />
id: GO:new<br />
name: chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed. Chlamydospores are larger than the standard spores produced by the fungus, have a <br />
very thick wall, and are usually darkly pigmented." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html]<br />
is_a: GO:0030435 ! sporulation<br />
<br />
id: GO:new<br />
name: asexual chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed from products of mitosis. Chlamydospores are larger than the standard spores produced <br />
by the fungus, have a very thick wall, and are usually darkly pigmented." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html] <br />
synonym: "chlamyodoconidium formation" EXACT [http://en.wikipedia.org/wiki/Chlamydospore]<br />
is_a: GO:0048315 ! conidium formation<br />
<br />
Another possibility, assuming that all chlamydospores are formed asexually after all:<br />
<br />
id: GO:new<br />
name: chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed. Chlamydospores are produced by hyphal fragmentation and are surrounded by a thick <br />
wall before separation." [GOC:mah, GOC:ds, ISBN:??]<br />
is_a: GO:0030435 ! sporulation<br />
<br />
</pre><br />
<br />
more defs that I'm reasonably confident of:<br />
<br />
<pre><br />
<br />
id: GO:0048315<br />
name: conidium formation<br />
def: "The process by which conidia, nonmotile asexual spores found in fungi, are formed. <br />
Conidia form on specialized structures called conidiophores, which may arise by conversion <br />
of hyphal elements or from specialized sporogenous cells." [ISBN:0963117211, PMID:2524423, <br />
PMID:9529886, http://www.ilmyco.gen.chicago.il.us/Terms/conid162.html]<br />
<br />
id: GO:new<br />
name: oidium formation<br />
def: "The process by which oidia, a type of asexual spore found in fungi, are formed. Oidia are <br />
borne a few at a time on very simple hyphae that protrude a short distance into the substrate, <br />
and are usually presumed not to constitute the main reproductive strategy of the fungus." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/oidiu163.html]<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: arthrospore formation<br />
def: "The formation of conidia by the conversion of a pre-existing hypha. An arthrospore is <br />
produced by the last cell on a hypha breaking off and dispersing. Usually the walls thicken <br />
and the cell(s) separates before swelling of each spore. Sometimes further septa form in each <br />
cell prior to disarticulation." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/arthr620.html, <br />
http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_a_b.shtml#arthrospore]<br />
synonym: "arthroconidium formation" EXACT [http://medical.merriam-webster.com/medical/medical?book=Medical&va=arthroconidium]<br />
is_a: GO:0048315 ! conidium formation<br />
Note: I also noticed some older papers (e.g. PMID: 618842) that use "arthrospore" to refer to a <br />
type of bacterial spore. Do we need to worry about that?<br />
<br />
id: GO:new<br />
name: blastospore formation<br />
def: "The formation of produced from a vegetative mother cell by budding. Blastospores <br />
are a type of asexual spore found in some fungi, including Candida species and the class <br />
Glomeromycota." [GOC:ds, ISBN:??]<br />
synonym: "blastoconidium formation" EXACT [http://cancerweb.ncl.ac.uk/cgi-bin/omd?Blastoconidium]<br />
is_a: GO:0048315 ! conidium formation<br />
<br />
id: GO:new<br />
name: sporangiospore formation<br />
def: "The process by which sporangiospores, a type of asexual spore found in fungi, are <br />
formed. Sporangiospores are formed within sac-like structure, the sporangium, following <br />
the division of the cytoplasm" [GOC:mah, GO:ds, <br />
http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_n_z.shtml]<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: endospore formation<br />
def: "The process by which a cell gives rise to an endospore, a dormant, highly resistant <br />
spore with a thick wall that forms within the mother cell. Endospores are produced by some <br />
low G+C Gram-positive bacteria in response to harsh conditions." [GOC:mah, GOC:ds, <br />
http://howie.myweb.uga.edu/introduction.html] <br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: akinete formation<br />
def: "The process by which an akinete, a thick-walled (encysted) dormant cell derived <br />
from the enlargement of a vegetative cell, is formed ''in several groups of Cyanobacteria''. Akinetes typically have granular <br />
cytoplasm." ''Akinetes are more resistant to environmental extremes than vegetative cells.'' [GOC:mah, GOC:ds, PMID:11948167, <br />
http://www.msu.edu/course/bot/423/algalglossary.htm#Reproductive]<br />
another def: <br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: myxospore formation<br />
def: The process by which differentiated, resting cells are formed usually within a fruiting body by Myxobacteria, usually within a fruiting body. The myxospore is more resistant to high temperature, dessication, and UV than vegetative myxobacteria. (encyclopedia of microbiology)<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: actinomycete-type spore formation?<br />
another def: Formation of differentiated, resting celsls from a substrate mycelium in many members of the order Actinomycetales. <br />
def: ?? might be able to use <br />
http://www.microbiologytext.com/index.php?module=Book&func=displayarticle&art_id=70 <br />
but need distinguishing features of the spores <br />
<br />
is_a: GO:0030436 ! asexual sporulation<br />
id: GO:0042243 (or GO:new)<br />
name: asexual spore wall formation<br />
def: "The chemical reactions and pathways resulting in the formation of the specialized <br />
envelope lying outside the cell membrane of a spore derived from a product of mitosis." [GOC:mah]<br />
(or 'spore wall formation, asexual', 'formation of asexual spore wall'?)<br />
<br />
id: GO:new<br />
name: sexual spore wall formation<br />
def: "The chemical reactions and pathways resulting in the formation of the specialized <br />
envelope lying outside the cell membrane of a spore derived from a product of meiosis." [GOC:mah]<br />
<br />
name changes only:<br />
id: GO:0030476<br />
name: ascospore wall assembly<br />
<br />
id: GO:0034217<br />
name: ascospore wall chitin biosynthetic process<br />
<br />
id: GO:0034218<br />
name: ascospore wall chitin metabolic process<br />
<br />
id: GO:0034232<br />
name: ascospore wall chitin catabolic process<br />
<br />
id: GO:0034223<br />
name: regulation of ascospore wall chitin biosynthetic process<br />
<br />
id: GO:0034234<br />
name: regulation of ascospore wall chitin catabolic process<br />
<br />
id: GO:0042763<br />
name: intracellular immature spore<br />
<br />
id: GO:0042764<br />
name: ascospore-type prospore?? check annotations<br />
<br />
<br />
</pre><br />
<br />
==March 7, 2008 ==<br />
<br />
(Midori)<br />
<br />
By email and at the last meeting (March 4th), we agreed to use GO:0030436 as the 'asexual sporulation' term rather than make it obsolete; ditto for GO:0042243 and spore walls. I've made other changes as agreed -- the parent 'sporulation' term is not under reproduction, but some of its children have additional parentage leading to reproduction, and additional relationships can be made if we've missed any sporulation types that should have paths to reproduction.<br />
<br />
I have not added any new 'chlamydospore' terms, but can do so once we've sorted out the existing 'chlamydospore development' term and whether we need another term for chlamydospores that are unambiguously regarded as spores.<br />
<br />
I also haven't added any new *spore wall assembly terms except GO:0034294, but can add terms as the need arises.<br />
<br />
<pre><br />
new terms<br />
sexual sporulation GO:0034293<br />
sexual spore wall assembly GO:0034294<br />
basidiospore formation GO:0034295<br />
zygospore formation GO:0034296<br />
oidium formation GO:0034297<br />
arthrospore formation GO:0034298<br />
blastospore formation GO:0034299<br />
sporangiospore formation GO:0034300<br />
endospore formation GO:0034301<br />
akinete formation GO:0034302<br />
myxospore formation GO:0034303<br />
actinomycete-type spore formation GO:0034304<br />
regulation of asexual sporulation GO:0034305<br />
regulation of sexual sporulation GO:0034306<br />
regulation of ascospore formation GO:0034307<br />
<br />
terms moved<br />
ascospore formation GO:0030437 to is_a GO:0034293<br />
conidium formation GO:0048315 to is_a GO:0030436<br />
</pre><br />
<br />
==March 18, 2008 Chlamydospores==<br />
(Debby)<br />
<br />
Based on the reading I've done chlamydospores are a mitotic spore formed by many different types of filamentous fungi. The 9th edition of Ainsworth & Bisby’s Dictionary of the Fungi (2001,ISBN:085199377X) gives the following definition for '''chlamydospore''': "an asexual 1-celled spore (primarily for perennation, not dissemination) originating endogenously and singly within part of a pre-existing cell, by the contraction of the protoplast and possessing an inner seconary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material. Originally proposed by de Bary in 1859 for ''Asterophora'' anamorphs. See Griffiths (''Nova Hedw.'' '''25''': 503, 1974; origin, structure, function), Hughes (''in'' Arai (Ed.), ''Filamentous microorganisms'': 1, 1985; definition, occurrence)."<br />
<br />
I suggest that GO term 'GO:0001410 chlamydospore development' be redefined so that it is inclusive of all fungal groups rather than being written specifically for Candida sp. and also that it be included under the parent term 'GO:0030435: sporulation'. The new definition could be based on the definition from Ainsworth & Bisby as follows: "a mitotic (asexual) 1-celled spore (primarily for survival, not dispersal) originating endogenously and singly within part of a pre-existing cell and possessing an inner secondary and often thickened cell wall." I've copied the current definition for term GO:0001410 below for comparison. <br />
<br />
id: GO:0001410<br />
name: chlamydospore development<br />
namespace: biological_process<br />
alt_id: GO:0055027<br />
def: "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. Chlamydospores are thick-walled, spore-like cells borne on the ends of elongated cells attached to hyphae or pseudohyphae, seen in the species Candida albicans and Candida dubliniensis. Note that although these structures resemble the chlamydospores of other fungi, it is not known whether they are true spores, so this process is not currently considered an instance of spore formation." [GOC:mcc, GOC:mtg_sensu, PMID:14663094]<br />
<br />
(Maria) I've just returned from a Candida meeting, and the exact nature of Candida chlamydospores is not understood. However, they do seem to be resting cells, and they can be isolated and germinated. The suggested definition above sounds like it would be appropriate.<br />
<br />
==April 2, 2008 Blastospores==<br />
(Maria)<br />
<br />
'Blastospore' is used in Candida species to mean 'yeast-form cell'; it's not a spore at all. We should definitely remove Candida from the definition. The web definition cited above ([http://cancerweb.ncl.ac.uk/cgi-bin/omd?Blastoconidium]) gives a yeast cell bud as an example of a blastospore. The etymology of 'blastospore' is 'bud spore' and maybe there are some real examples of spores that arise this way, but not in Candida. Do we need to add this term at all? I thought that in general, we were aiming to establish a correct structure for the ontology but not to think of every possible term that might be needed for new species in the future.<br />
<br />
==March 18, 2008 Akinetes==</div>Mariahttps://wiki.geneontology.org/index.php?title=Sporulation_Meeting_Notes&diff=12201Sporulation Meeting Notes2008-04-02T14:34:50Z<p>Maria: /* March 18, 2008 Chlamydospores */</p>
<hr />
<div>==August 2007 - January 2008==<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
== Feb. 14, 2008 ==<br />
<br />
'''Midori''' (very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
:updated earlier draft; see Definitions below<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:''' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
==February 20, 2008 Skype "meeting"==<br />
Present: Midori, Debby, Maria, Pascale, Val<br />
<br />
===Meeting summary===<br />
(Midori)<br />
<br />
We discussed whether sporulation should go under reproduction; it's not resolved yet, but the other changes don't depend on the decision. If sporulation (GO:0030435) itself doesn't go under reproduction, descendants of sporulation can have reproduction as an additional parent as needed.<br />
<br />
Changes we did decide on:<br />
<br />
*Create two child terms, for spores produced by mitosis (= asexual) and by meiosis (sexual), The definitions probably need work; any other comments also welcome. Definitions below.<br />
*For types of sporulation observed in bacteria, Debby will look up distinguishing features that can be used in definitions; Midori will help convert that information into GO-definition-friendly sentences. See below ...<br />
*Rename 30437 to ascospore formation, and improve definition; also rename 30476 to ascospore wall assembly.<br />
*Move conidium formation (GO:0048315) to is_a mitotic/asexual sporulation. <br />
*We agreed to make three terms obsolete:<br />
**reproductive sporulation GO:0048622<br />
::This term is ill defined, so much so that we don't know what it was intended to mean; it also has a parent (reproductive process in single-celled organism) that isn't consistent with the 'sporulation whose primary biological objective is reproduction' meaning (true path violation - cf ferns, mosses, mushrooms). No gene products are annotated directly to GO:0048622<br />
:*sporulation (sensu Bacteria) GO:0030436<br />
::This is a grouping term that isn't useful -- there are several different types of spore formed by different species/genera/etc. of bacteria, and there is neither a need nor a good basis for grouping them with each other.<br />
:*spore wall assembly (sensu Bacteria) GO:0042243<br />
::Reasons analogous to those given for GO:0030436 above.<br />
<br />
<br />
'''Debby''' 2/20/08<br />
<br />
GO:0030435 sporulation<br />
<br />
*Sexual or meiotic spores (child term of sporulation) <br />
** Ascospores (meiotically produced spores form by Ascomycetes)<br />
** Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
** Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
** Ferns<br />
<br />
*Asexual or mitotic spores (child term of sporulation) <br />
**Arthrospores (aka oidia)(Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
**Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
**Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott) <br />
**Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes) <br />
**Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
**Dictyostelium - forms spores inside fruiting bodies<br />
**Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some low G+C Gram-positive bacteria)<br />
**Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.) <br />
**Myxospore<br />
**Actinomycetes (High G+C Gram-positive bacteria that form spores)<br />
<br />
'''Midori:''' Current draft of the proposed ontology structure (Feb. 20):<br />
<br />
sporulation GO:0030436<br><br />
[i] asexual sporulation GO:new<br><br />
--[i] conidium formation GO:0048315<br><br />
--[new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
[i] sexual sporulation GO:new<br />
--[i] ascospore formation GO:0030437 (renamed)<br><br />
-- --[p] ascospore wall formation GO:0030476 (renamed)<br><br />
-- --[p] ascospore-type prospore formation GO:0031321 (renamed; suggestions welcome for nicer new name)<br><br />
--[other new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
--[p] spore wall assembly GO:0042244<br><br />
-- --[i] ascospore wall formation GO:0030476 (renamed)<br><br />
-- --[other new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
<br />
===Definitions===<br />
(Feb. 26; Midori)<br />
(minor updates March 7; Midori)<br />
<br />
<pre><br />
id: GO:0030435<br />
name: sporulation<br />
def: "The process by which a relatively unspecialized cell acquires the specialized features <br />
of a spore, a cell form that can be used for dissemination, for survival of adverse conditions <br />
because of its heat and dessication resistance, and/or for reproduction.Spores are usually <br />
unicellular and may develop into vegetative organisms or gametes. They may be produced <br />
asexually or sexually and are of many types." [GOC:mah; ISBN:0072992913]<br />
<br />
id: GO:0030436<br />
name: asexual sporulation<br />
def: "The formation of spores derived from the products of mitosis." [GOC:mah; PMID: 9529886]<br />
synonym: "asexual spore formation" EXACT []<br />
synonym: "mitotic sporulation" EXACT []<br />
synonym: "mitotic spore formation" EXACT []<br />
synonym: "spore formation (sensu Bacteria)" NARROW []<br />
synonym: "sporulation (sensu Bacteria)" NARROW []<br />
is_a: GO:0030435 ! sporulation<br />
<br />
id: GO:new<br />
name: sexual sporulation<br />
def: "The formation of spores derived from the products of meiosis." [GOC:mah]<br />
synonym: "meiotic sporulation" EXACT []<br />
synonym: "meiotic spore formation" EXACT []<br />
synonym: "sexual spore formation" EXACT []<br />
is_a: GO:0030435 ! sporulation<br />
<br />
Note: any of the synonyms could be used as the term name, if you prefer.<br />
<br />
id: GO:0030437<br />
name: ascospore formation<br />
def: "The process by which a diploid cell undergoes meiosis, and the meiotic products <br />
acquire the specialized features of ascospores. Ascospores are generally found in clusters <br />
of four or eight spores within a single mother cell, the ascus, and are characteristic of the <br />
ascomycete fungi (phylum Ascomycota)." [GOC:mah; PMID:16339736]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
id: GO:new<br />
name: basidiospore formation<br />
def: "The process by which spores form outside a specialized end cell known as a basidium. <br />
Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to <br />
spores that each contain a haploid nucleus that is the product of meiosis. The spores are <br />
usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In <br />
most basidiomycetes there are four sterigmata (and four spores) to a basidium." [GOC:mah, <br />
GOC:ds, http://www.ilmyco.gen.chicago.il.us/Terms/basid133.html, <br />
http://www.gsbs.utmb.edu/microbook/ch073.htm]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
id: GO:new<br />
name: zygospore formation<br />
def: "The process by which zygospores are formed. Zygospores are characteristic of the <br />
zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily <br />
ornamented as well, with many spines or ridges. It is formed between two specialized organs <br />
called suspensors, which are themselves usually heavily ornamented, one from each mating <br />
partner. The zygospore forms between them and then breaks away." [GOC:mah, GOC:ds, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/zygos581.html]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
</pre><br />
<br />
more Feb. 28 (Midori)<br />
<br />
I think some of these are likely to require more work, because different sources don't quite agree on some things, especially for "chlamydospore" -- the Illinois Mycological Association fungal term glossary says that chlamydospores can be sexual or asexual. I'm also not sure where the part about hyphal fragmentation that Debby found in Prescott belongs. And we also have to deal with the existing term 'chlamydospore developmen GO:0001410, which is defined and used for structures in Candida that may not be true spores.<br />
<br />
I've concocted two possible versions, with one or two chlamydospore formation terms (note that neither option considers the GO:0001410 wrinkle).<br />
<br />
refs: PMID: 16215181, http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html, the wiki and sources noted therein<br />
<br />
<pre><br />
<br />
One possibility:<br />
id: GO:new<br />
name: chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed. Chlamydospores are larger than the standard spores produced by the fungus, have a <br />
very thick wall, and are usually darkly pigmented." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html]<br />
is_a: GO:0030435 ! sporulation<br />
<br />
id: GO:new<br />
name: asexual chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed from products of mitosis. Chlamydospores are larger than the standard spores produced <br />
by the fungus, have a very thick wall, and are usually darkly pigmented." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html] <br />
synonym: "chlamyodoconidium formation" EXACT [http://en.wikipedia.org/wiki/Chlamydospore]<br />
is_a: GO:0048315 ! conidium formation<br />
<br />
Another possibility, assuming that all chlamydospores are formed asexually after all:<br />
<br />
id: GO:new<br />
name: chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed. Chlamydospores are produced by hyphal fragmentation and are surrounded by a thick <br />
wall before separation." [GOC:mah, GOC:ds, ISBN:??]<br />
is_a: GO:0030435 ! sporulation<br />
<br />
</pre><br />
<br />
more defs that I'm reasonably confident of:<br />
<br />
<pre><br />
<br />
id: GO:0048315<br />
name: conidium formation<br />
def: "The process by which conidia, nonmotile asexual spores found in fungi, are formed. <br />
Conidia form on specialized structures called conidiophores, which may arise by conversion <br />
of hyphal elements or from specialized sporogenous cells." [ISBN:0963117211, PMID:2524423, <br />
PMID:9529886, http://www.ilmyco.gen.chicago.il.us/Terms/conid162.html]<br />
<br />
id: GO:new<br />
name: oidium formation<br />
def: "The process by which oidia, a type of asexual spore found in fungi, are formed. Oidia are <br />
borne a few at a time on very simple hyphae that protrude a short distance into the substrate, <br />
and are usually presumed not to constitute the main reproductive strategy of the fungus." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/oidiu163.html]<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: arthrospore formation<br />
def: "The formation of conidia by the conversion of a pre-existing hypha. An arthrospore is <br />
produced by the last cell on a hypha breaking off and dispersing. Usually the walls thicken <br />
and the cell(s) separates before swelling of each spore. Sometimes further septa form in each <br />
cell prior to disarticulation." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/arthr620.html, <br />
http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_a_b.shtml#arthrospore]<br />
synonym: "arthroconidium formation" EXACT [http://medical.merriam-webster.com/medical/medical?book=Medical&va=arthroconidium]<br />
is_a: GO:0048315 ! conidium formation<br />
Note: I also noticed some older papers (e.g. PMID: 618842) that use "arthrospore" to refer to a <br />
type of bacterial spore. Do we need to worry about that?<br />
<br />
id: GO:new<br />
name: blastospore formation<br />
def: "The formation of produced from a vegetative mother cell by budding. Blastospores <br />
are a type of asexual spore found in some fungi, including Candida species and the class <br />
Glomeromycota." [GOC:ds, ISBN:??]<br />
synonym: "blastoconidium formation" EXACT [http://cancerweb.ncl.ac.uk/cgi-bin/omd?Blastoconidium]<br />
is_a: GO:0048315 ! conidium formation<br />
<br />
id: GO:new<br />
name: sporangiospore formation<br />
def: "The process by which sporangiospores, a type of asexual spore found in fungi, are <br />
formed. Sporangiospores are formed within sac-like structure, the sporangium, following <br />
the division of the cytoplasm" [GOC:mah, GO:ds, <br />
http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_n_z.shtml]<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: endospore formation<br />
def: "The process by which a cell gives rise to an endospore, a dormant, highly resistant <br />
spore with a thick wall that forms within the mother cell. Endospores are produced by some <br />
low G+C Gram-positive bacteria in response to harsh conditions." [GOC:mah, GOC:ds, <br />
http://howie.myweb.uga.edu/introduction.html] <br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: akinete formation<br />
def: "The process by which an akinete, a thick-walled (encysted) dormant cell derived <br />
from the enlargement of a vegetative cell, is formed ''in several groups of Cyanobacteria''. Akinetes typically have granular <br />
cytoplasm." ''Akinetes are more resistant to environmental extremes than vegetative cells.'' [GOC:mah, GOC:ds, PMID:11948167, <br />
http://www.msu.edu/course/bot/423/algalglossary.htm#Reproductive]<br />
another def: <br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: myxospore formation<br />
def: The process by which differentiated, resting cells are formed usually within a fruiting body by Myxobacteria, usually within a fruiting body. The myxospore is more resistant to high temperature, dessication, and UV than vegetative myxobacteria. (encyclopedia of microbiology)<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: actinomycete-type spore formation?<br />
another def: Formation of differentiated, resting celsls from a substrate mycelium in many members of the order Actinomycetales. <br />
def: ?? might be able to use <br />
http://www.microbiologytext.com/index.php?module=Book&func=displayarticle&art_id=70 <br />
but need distinguishing features of the spores <br />
<br />
is_a: GO:0030436 ! asexual sporulation<br />
id: GO:0042243 (or GO:new)<br />
name: asexual spore wall formation<br />
def: "The chemical reactions and pathways resulting in the formation of the specialized <br />
envelope lying outside the cell membrane of a spore derived from a product of mitosis." [GOC:mah]<br />
(or 'spore wall formation, asexual', 'formation of asexual spore wall'?)<br />
<br />
id: GO:new<br />
name: sexual spore wall formation<br />
def: "The chemical reactions and pathways resulting in the formation of the specialized <br />
envelope lying outside the cell membrane of a spore derived from a product of meiosis." [GOC:mah]<br />
<br />
name changes only:<br />
id: GO:0030476<br />
name: ascospore wall assembly<br />
<br />
id: GO:0034217<br />
name: ascospore wall chitin biosynthetic process<br />
<br />
id: GO:0034218<br />
name: ascospore wall chitin metabolic process<br />
<br />
id: GO:0034232<br />
name: ascospore wall chitin catabolic process<br />
<br />
id: GO:0034223<br />
name: regulation of ascospore wall chitin biosynthetic process<br />
<br />
id: GO:0034234<br />
name: regulation of ascospore wall chitin catabolic process<br />
<br />
id: GO:0042763<br />
name: intracellular immature spore<br />
<br />
id: GO:0042764<br />
name: ascospore-type prospore?? check annotations<br />
<br />
<br />
</pre><br />
<br />
==March 7, 2008 ==<br />
<br />
(Midori)<br />
<br />
By email and at the last meeting (March 4th), we agreed to use GO:0030436 as the 'asexual sporulation' term rather than make it obsolete; ditto for GO:0042243 and spore walls. I've made other changes as agreed -- the parent 'sporulation' term is not under reproduction, but some of its children have additional parentage leading to reproduction, and additional relationships can be made if we've missed any sporulation types that should have paths to reproduction.<br />
<br />
I have not added any new 'chlamydospore' terms, but can do so once we've sorted out the existing 'chlamydospore development' term and whether we need another term for chlamydospores that are unambiguously regarded as spores.<br />
<br />
I also haven't added any new *spore wall assembly terms except GO:0034294, but can add terms as the need arises.<br />
<br />
<pre><br />
new terms<br />
sexual sporulation GO:0034293<br />
sexual spore wall assembly GO:0034294<br />
basidiospore formation GO:0034295<br />
zygospore formation GO:0034296<br />
oidium formation GO:0034297<br />
arthrospore formation GO:0034298<br />
blastospore formation GO:0034299<br />
sporangiospore formation GO:0034300<br />
endospore formation GO:0034301<br />
akinete formation GO:0034302<br />
myxospore formation GO:0034303<br />
actinomycete-type spore formation GO:0034304<br />
regulation of asexual sporulation GO:0034305<br />
regulation of sexual sporulation GO:0034306<br />
regulation of ascospore formation GO:0034307<br />
<br />
terms moved<br />
ascospore formation GO:0030437 to is_a GO:0034293<br />
conidium formation GO:0048315 to is_a GO:0030436<br />
</pre><br />
<br />
==March 18, 2008 Chlamydospores==<br />
(Debby)<br />
<br />
Based on the reading I've done chlamydospores are a mitotic spore formed by many different types of filamentous fungi. The 9th edition of Ainsworth & Bisby’s Dictionary of the Fungi (2001,ISBN:085199377X) gives the following definition for '''chlamydospore''': "an asexual 1-celled spore (primarily for perennation, not dissemination) originating endogenously and singly within part of a pre-existing cell, by the contraction of the protoplast and possessing an inner seconary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material. Originally proposed by de Bary in 1859 for ''Asterophora'' anamorphs. See Griffiths (''Nova Hedw.'' '''25''': 503, 1974; origin, structure, function), Hughes (''in'' Arai (Ed.), ''Filamentous microorganisms'': 1, 1985; definition, occurrence)."<br />
<br />
I suggest that GO term 'GO:0001410 chlamydospore development' be redefined so that it is inclusive of all fungal groups rather than being written specifically for Candida sp. and also that it be included under the parent term 'GO:0030435: sporulation'. The new definition could be based on the definition from Ainsworth & Bisby as follows: "a mitotic (asexual) 1-celled spore (primarily for survival, not dispersal) originating endogenously and singly within part of a pre-existing cell and possessing an inner secondary and often thickened cell wall." I've copied the current definition for term GO:0001410 below for comparison. <br />
<br />
id: GO:0001410<br />
name: chlamydospore development<br />
namespace: biological_process<br />
alt_id: GO:0055027<br />
def: "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. Chlamydospores are thick-walled, spore-like cells borne on the ends of elongated cells attached to hyphae or pseudohyphae, seen in the species Candida albicans and Candida dubliniensis. Note that although these structures resemble the chlamydospores of other fungi, it is not known whether they are true spores, so this process is not currently considered an instance of spore formation." [GOC:mcc, GOC:mtg_sensu, PMID:14663094]<br />
<br />
(Maria) I've just returned from a Candida meeting, and the exact nature of Candida chlamydospores is not understood. However, they do seem to be resting cells, and they can be isolated and germinated. The suggested definition above sounds like it would be appropriate.<br />
<br />
==April 2, 2008 Blastospores==<br />
(Maria)<br />
<br />
'Blastospore' is used in Candida species to mean 'yeast-form cell'; it's not a spore at all. We should definitely remove Candida from the definition.<br />
<br />
==March 18, 2008 Akinetes==</div>Mariahttps://wiki.geneontology.org/index.php?title=Sporulation_Meeting_Notes&diff=12200Sporulation Meeting Notes2008-04-02T14:27:38Z<p>Maria: /* March 18, 2008 Chlamydospores */</p>
<hr />
<div>==August 2007 - January 2008==<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
== Feb. 14, 2008 ==<br />
<br />
'''Midori''' (very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
:updated earlier draft; see Definitions below<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:''' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
==February 20, 2008 Skype "meeting"==<br />
Present: Midori, Debby, Maria, Pascale, Val<br />
<br />
===Meeting summary===<br />
(Midori)<br />
<br />
We discussed whether sporulation should go under reproduction; it's not resolved yet, but the other changes don't depend on the decision. If sporulation (GO:0030435) itself doesn't go under reproduction, descendants of sporulation can have reproduction as an additional parent as needed.<br />
<br />
Changes we did decide on:<br />
<br />
*Create two child terms, for spores produced by mitosis (= asexual) and by meiosis (sexual), The definitions probably need work; any other comments also welcome. Definitions below.<br />
*For types of sporulation observed in bacteria, Debby will look up distinguishing features that can be used in definitions; Midori will help convert that information into GO-definition-friendly sentences. See below ...<br />
*Rename 30437 to ascospore formation, and improve definition; also rename 30476 to ascospore wall assembly.<br />
*Move conidium formation (GO:0048315) to is_a mitotic/asexual sporulation. <br />
*We agreed to make three terms obsolete:<br />
**reproductive sporulation GO:0048622<br />
::This term is ill defined, so much so that we don't know what it was intended to mean; it also has a parent (reproductive process in single-celled organism) that isn't consistent with the 'sporulation whose primary biological objective is reproduction' meaning (true path violation - cf ferns, mosses, mushrooms). No gene products are annotated directly to GO:0048622<br />
:*sporulation (sensu Bacteria) GO:0030436<br />
::This is a grouping term that isn't useful -- there are several different types of spore formed by different species/genera/etc. of bacteria, and there is neither a need nor a good basis for grouping them with each other.<br />
:*spore wall assembly (sensu Bacteria) GO:0042243<br />
::Reasons analogous to those given for GO:0030436 above.<br />
<br />
<br />
'''Debby''' 2/20/08<br />
<br />
GO:0030435 sporulation<br />
<br />
*Sexual or meiotic spores (child term of sporulation) <br />
** Ascospores (meiotically produced spores form by Ascomycetes)<br />
** Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
** Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
** Ferns<br />
<br />
*Asexual or mitotic spores (child term of sporulation) <br />
**Arthrospores (aka oidia)(Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
**Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
**Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott) <br />
**Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes) <br />
**Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
**Dictyostelium - forms spores inside fruiting bodies<br />
**Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some low G+C Gram-positive bacteria)<br />
**Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.) <br />
**Myxospore<br />
**Actinomycetes (High G+C Gram-positive bacteria that form spores)<br />
<br />
'''Midori:''' Current draft of the proposed ontology structure (Feb. 20):<br />
<br />
sporulation GO:0030436<br><br />
[i] asexual sporulation GO:new<br><br />
--[i] conidium formation GO:0048315<br><br />
--[new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
[i] sexual sporulation GO:new<br />
--[i] ascospore formation GO:0030437 (renamed)<br><br />
-- --[p] ascospore wall formation GO:0030476 (renamed)<br><br />
-- --[p] ascospore-type prospore formation GO:0031321 (renamed; suggestions welcome for nicer new name)<br><br />
--[other new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
--[p] spore wall assembly GO:0042244<br><br />
-- --[i] ascospore wall formation GO:0030476 (renamed)<br><br />
-- --[other new terms as needed, e.g. as in Feb. 14 draft above]<br><br />
<br />
===Definitions===<br />
(Feb. 26; Midori)<br />
(minor updates March 7; Midori)<br />
<br />
<pre><br />
id: GO:0030435<br />
name: sporulation<br />
def: "The process by which a relatively unspecialized cell acquires the specialized features <br />
of a spore, a cell form that can be used for dissemination, for survival of adverse conditions <br />
because of its heat and dessication resistance, and/or for reproduction.Spores are usually <br />
unicellular and may develop into vegetative organisms or gametes. They may be produced <br />
asexually or sexually and are of many types." [GOC:mah; ISBN:0072992913]<br />
<br />
id: GO:0030436<br />
name: asexual sporulation<br />
def: "The formation of spores derived from the products of mitosis." [GOC:mah; PMID: 9529886]<br />
synonym: "asexual spore formation" EXACT []<br />
synonym: "mitotic sporulation" EXACT []<br />
synonym: "mitotic spore formation" EXACT []<br />
synonym: "spore formation (sensu Bacteria)" NARROW []<br />
synonym: "sporulation (sensu Bacteria)" NARROW []<br />
is_a: GO:0030435 ! sporulation<br />
<br />
id: GO:new<br />
name: sexual sporulation<br />
def: "The formation of spores derived from the products of meiosis." [GOC:mah]<br />
synonym: "meiotic sporulation" EXACT []<br />
synonym: "meiotic spore formation" EXACT []<br />
synonym: "sexual spore formation" EXACT []<br />
is_a: GO:0030435 ! sporulation<br />
<br />
Note: any of the synonyms could be used as the term name, if you prefer.<br />
<br />
id: GO:0030437<br />
name: ascospore formation<br />
def: "The process by which a diploid cell undergoes meiosis, and the meiotic products <br />
acquire the specialized features of ascospores. Ascospores are generally found in clusters <br />
of four or eight spores within a single mother cell, the ascus, and are characteristic of the <br />
ascomycete fungi (phylum Ascomycota)." [GOC:mah; PMID:16339736]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
id: GO:new<br />
name: basidiospore formation<br />
def: "The process by which spores form outside a specialized end cell known as a basidium. <br />
Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to <br />
spores that each contain a haploid nucleus that is the product of meiosis. The spores are <br />
usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In <br />
most basidiomycetes there are four sterigmata (and four spores) to a basidium." [GOC:mah, <br />
GOC:ds, http://www.ilmyco.gen.chicago.il.us/Terms/basid133.html, <br />
http://www.gsbs.utmb.edu/microbook/ch073.htm]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
id: GO:new<br />
name: zygospore formation<br />
def: "The process by which zygospores are formed. Zygospores are characteristic of the <br />
zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily <br />
ornamented as well, with many spines or ridges. It is formed between two specialized organs <br />
called suspensors, which are themselves usually heavily ornamented, one from each mating <br />
partner. The zygospore forms between them and then breaks away." [GOC:mah, GOC:ds, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/zygos581.html]<br />
is_a: GO:new ! sexual sporulation<br />
<br />
</pre><br />
<br />
more Feb. 28 (Midori)<br />
<br />
I think some of these are likely to require more work, because different sources don't quite agree on some things, especially for "chlamydospore" -- the Illinois Mycological Association fungal term glossary says that chlamydospores can be sexual or asexual. I'm also not sure where the part about hyphal fragmentation that Debby found in Prescott belongs. And we also have to deal with the existing term 'chlamydospore developmen GO:0001410, which is defined and used for structures in Candida that may not be true spores.<br />
<br />
I've concocted two possible versions, with one or two chlamydospore formation terms (note that neither option considers the GO:0001410 wrinkle).<br />
<br />
refs: PMID: 16215181, http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html, the wiki and sources noted therein<br />
<br />
<pre><br />
<br />
One possibility:<br />
id: GO:new<br />
name: chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed. Chlamydospores are larger than the standard spores produced by the fungus, have a <br />
very thick wall, and are usually darkly pigmented." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html]<br />
is_a: GO:0030435 ! sporulation<br />
<br />
id: GO:new<br />
name: asexual chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed from products of mitosis. Chlamydospores are larger than the standard spores produced <br />
by the fungus, have a very thick wall, and are usually darkly pigmented." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/chlam385.html] <br />
synonym: "chlamyodoconidium formation" EXACT [http://en.wikipedia.org/wiki/Chlamydospore]<br />
is_a: GO:0048315 ! conidium formation<br />
<br />
Another possibility, assuming that all chlamydospores are formed asexually after all:<br />
<br />
id: GO:new<br />
name: chlamydospore formation<br />
def: "The process by which chlamydospores, a specialized type of spore found in fungi, are <br />
formed. Chlamydospores are produced by hyphal fragmentation and are surrounded by a thick <br />
wall before separation." [GOC:mah, GOC:ds, ISBN:??]<br />
is_a: GO:0030435 ! sporulation<br />
<br />
</pre><br />
<br />
more defs that I'm reasonably confident of:<br />
<br />
<pre><br />
<br />
id: GO:0048315<br />
name: conidium formation<br />
def: "The process by which conidia, nonmotile asexual spores found in fungi, are formed. <br />
Conidia form on specialized structures called conidiophores, which may arise by conversion <br />
of hyphal elements or from specialized sporogenous cells." [ISBN:0963117211, PMID:2524423, <br />
PMID:9529886, http://www.ilmyco.gen.chicago.il.us/Terms/conid162.html]<br />
<br />
id: GO:new<br />
name: oidium formation<br />
def: "The process by which oidia, a type of asexual spore found in fungi, are formed. Oidia are <br />
borne a few at a time on very simple hyphae that protrude a short distance into the substrate, <br />
and are usually presumed not to constitute the main reproductive strategy of the fungus." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/oidiu163.html]<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: arthrospore formation<br />
def: "The formation of conidia by the conversion of a pre-existing hypha. An arthrospore is <br />
produced by the last cell on a hypha breaking off and dispersing. Usually the walls thicken <br />
and the cell(s) separates before swelling of each spore. Sometimes further septa form in each <br />
cell prior to disarticulation." [GOC:mah, <br />
http://www.ilmyco.gen.chicago.il.us/Terms/arthr620.html, <br />
http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_a_b.shtml#arthrospore]<br />
synonym: "arthroconidium formation" EXACT [http://medical.merriam-webster.com/medical/medical?book=Medical&va=arthroconidium]<br />
is_a: GO:0048315 ! conidium formation<br />
Note: I also noticed some older papers (e.g. PMID: 618842) that use "arthrospore" to refer to a <br />
type of bacterial spore. Do we need to worry about that?<br />
<br />
id: GO:new<br />
name: blastospore formation<br />
def: "The formation of produced from a vegetative mother cell by budding. Blastospores <br />
are a type of asexual spore found in some fungi, including Candida species and the class <br />
Glomeromycota." [GOC:ds, ISBN:??]<br />
synonym: "blastoconidium formation" EXACT [http://cancerweb.ncl.ac.uk/cgi-bin/omd?Blastoconidium]<br />
is_a: GO:0048315 ! conidium formation<br />
<br />
id: GO:new<br />
name: sporangiospore formation<br />
def: "The process by which sporangiospores, a type of asexual spore found in fungi, are <br />
formed. Sporangiospores are formed within sac-like structure, the sporangium, following <br />
the division of the cytoplasm" [GOC:mah, GO:ds, <br />
http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_n_z.shtml]<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: endospore formation<br />
def: "The process by which a cell gives rise to an endospore, a dormant, highly resistant <br />
spore with a thick wall that forms within the mother cell. Endospores are produced by some <br />
low G+C Gram-positive bacteria in response to harsh conditions." [GOC:mah, GOC:ds, <br />
http://howie.myweb.uga.edu/introduction.html] <br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: akinete formation<br />
def: "The process by which an akinete, a thick-walled (encysted) dormant cell derived <br />
from the enlargement of a vegetative cell, is formed ''in several groups of Cyanobacteria''. Akinetes typically have granular <br />
cytoplasm." ''Akinetes are more resistant to environmental extremes than vegetative cells.'' [GOC:mah, GOC:ds, PMID:11948167, <br />
http://www.msu.edu/course/bot/423/algalglossary.htm#Reproductive]<br />
another def: <br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: myxospore formation<br />
def: The process by which differentiated, resting cells are formed usually within a fruiting body by Myxobacteria, usually within a fruiting body. The myxospore is more resistant to high temperature, dessication, and UV than vegetative myxobacteria. (encyclopedia of microbiology)<br />
is_a: GO:0030436 ! asexual sporulation<br />
<br />
id: GO:new<br />
name: actinomycete-type spore formation?<br />
another def: Formation of differentiated, resting celsls from a substrate mycelium in many members of the order Actinomycetales. <br />
def: ?? might be able to use <br />
http://www.microbiologytext.com/index.php?module=Book&func=displayarticle&art_id=70 <br />
but need distinguishing features of the spores <br />
<br />
is_a: GO:0030436 ! asexual sporulation<br />
id: GO:0042243 (or GO:new)<br />
name: asexual spore wall formation<br />
def: "The chemical reactions and pathways resulting in the formation of the specialized <br />
envelope lying outside the cell membrane of a spore derived from a product of mitosis." [GOC:mah]<br />
(or 'spore wall formation, asexual', 'formation of asexual spore wall'?)<br />
<br />
id: GO:new<br />
name: sexual spore wall formation<br />
def: "The chemical reactions and pathways resulting in the formation of the specialized <br />
envelope lying outside the cell membrane of a spore derived from a product of meiosis." [GOC:mah]<br />
<br />
name changes only:<br />
id: GO:0030476<br />
name: ascospore wall assembly<br />
<br />
id: GO:0034217<br />
name: ascospore wall chitin biosynthetic process<br />
<br />
id: GO:0034218<br />
name: ascospore wall chitin metabolic process<br />
<br />
id: GO:0034232<br />
name: ascospore wall chitin catabolic process<br />
<br />
id: GO:0034223<br />
name: regulation of ascospore wall chitin biosynthetic process<br />
<br />
id: GO:0034234<br />
name: regulation of ascospore wall chitin catabolic process<br />
<br />
id: GO:0042763<br />
name: intracellular immature spore<br />
<br />
id: GO:0042764<br />
name: ascospore-type prospore?? check annotations<br />
<br />
<br />
</pre><br />
<br />
==March 7, 2008 ==<br />
<br />
(Midori)<br />
<br />
By email and at the last meeting (March 4th), we agreed to use GO:0030436 as the 'asexual sporulation' term rather than make it obsolete; ditto for GO:0042243 and spore walls. I've made other changes as agreed -- the parent 'sporulation' term is not under reproduction, but some of its children have additional parentage leading to reproduction, and additional relationships can be made if we've missed any sporulation types that should have paths to reproduction.<br />
<br />
I have not added any new 'chlamydospore' terms, but can do so once we've sorted out the existing 'chlamydospore development' term and whether we need another term for chlamydospores that are unambiguously regarded as spores.<br />
<br />
I also haven't added any new *spore wall assembly terms except GO:0034294, but can add terms as the need arises.<br />
<br />
<pre><br />
new terms<br />
sexual sporulation GO:0034293<br />
sexual spore wall assembly GO:0034294<br />
basidiospore formation GO:0034295<br />
zygospore formation GO:0034296<br />
oidium formation GO:0034297<br />
arthrospore formation GO:0034298<br />
blastospore formation GO:0034299<br />
sporangiospore formation GO:0034300<br />
endospore formation GO:0034301<br />
akinete formation GO:0034302<br />
myxospore formation GO:0034303<br />
actinomycete-type spore formation GO:0034304<br />
regulation of asexual sporulation GO:0034305<br />
regulation of sexual sporulation GO:0034306<br />
regulation of ascospore formation GO:0034307<br />
<br />
terms moved<br />
ascospore formation GO:0030437 to is_a GO:0034293<br />
conidium formation GO:0048315 to is_a GO:0030436<br />
</pre><br />
<br />
==March 18, 2008 Chlamydospores==<br />
(Debby)<br />
<br />
Based on the reading I've done chlamydospores are a mitotic spore formed by many different types of filamentous fungi. The 9th edition of Ainsworth & Bisby’s Dictionary of the Fungi (2001,ISBN:085199377X) gives the following definition for '''chlamydospore''': "an asexual 1-celled spore (primarily for perennation, not dissemination) originating endogenously and singly within part of a pre-existing cell, by the contraction of the protoplast and possessing an inner seconary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material. Originally proposed by de Bary in 1859 for ''Asterophora'' anamorphs. See Griffiths (''Nova Hedw.'' '''25''': 503, 1974; origin, structure, function), Hughes (''in'' Arai (Ed.), ''Filamentous microorganisms'': 1, 1985; definition, occurrence)."<br />
<br />
I suggest that GO term 'GO:0001410 chlamydospore development' be redefined so that it is inclusive of all fungal groups rather than being written specifically for Candida sp. and also that it be included under the parent term 'GO:0030435: sporulation'. The new definition could be based on the definition from Ainsworth & Bisby as follows: "a mitotic (asexual) 1-celled spore (primarily for survival, not dispersal) originating endogenously and singly within part of a pre-existing cell and possessing an inner secondary and often thickened cell wall." I've copied the current definition for term GO:0001410 below for comparison. <br />
<br />
id: GO:0001410<br />
name: chlamydospore development<br />
namespace: biological_process<br />
alt_id: GO:0055027<br />
def: "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. Chlamydospores are thick-walled, spore-like cells borne on the ends of elongated cells attached to hyphae or pseudohyphae, seen in the species Candida albicans and Candida dubliniensis. Note that although these structures resemble the chlamydospores of other fungi, it is not known whether they are true spores, so this process is not currently considered an instance of spore formation." [GOC:mcc, GOC:mtg_sensu, PMID:14663094]<br />
<br />
(Maria) I've just returned from a Candida meeting, and the exact nature of Candida chlamydospores is not understood. However, they do seem to be resting cells, and they can be isolated and germinated. The suggested definition above sounds like it would be appropriate.<br />
<br />
==March 18, 2008 Akinetes==</div>Mariahttps://wiki.geneontology.org/index.php?title=External_Database_Contact_Info_(Archived)&diff=12152External Database Contact Info (Archived)2008-03-28T23:52:17Z<p>Maria: </p>
<hr />
<div>Many groups associated with and outside the GOC consume the resources produced by GO, such as the gene_ontology_edit.obo file and the association files. Any major changes to these files are signaled in advanced on the gofriends list. We also would like to track the persons in charge of the technical aspects of the various different MOD databases in order to make sure they are prepared for forthcoming changes.<br />
<br />
== dictyBase ==<br />
<br />
* siddhartha-basu AT northwestern DOT edu<br />
* pgaudet AT northwestern DOT edu<br />
<br />
Schema: Chado<br />
<br />
== SGD ==<br />
<br />
* Mike Cherry (cherry AT stanford DOT edu)<br />
* Ben Hitz ( hitz AT genome DOT stanford AT edu)<br />
* Eurie Hong (eurie AT genome DOT stanford DOT edu)<br />
* Gail Binkley (gail AT genome DOT stanford DOT edu)<br />
* GO-ADMIN (go-admin AT genome DOT stanford DOT edu)<br />
<br />
== RGD ==<br />
<br />
Curation<br />
* Victoria Petri vpetri at mcw dot edu<br />
* Mary Shimoyama shimoyama at mcw dot edu<br />
<br />
Technical<br />
* Alex Stoddard (astoddard at mcw dot edu)<br />
<br />
Admin<br />
* Simon Twigger simont at mcw dot edu<br />
<br />
== MGI ==<br />
<br />
* David Miers <dbm AT informatics DOT jax DOT org><br />
* Jim Kadin <jak AT informatics DOT jax DOT org><br />
* David Hill <dph AT informatics DOT jax DOT org><br />
<br />
==UniProtKB ==<br />
<br />
* Dan Barrell<br />
* David Binns<br />
<br />
== WormBase ==<br />
* Ranjana Kishore <ranjana@caltech.edu><br />
* Kimberly Van Auken <vanauken@caltech.edu><br />
<br />
== FlyBase ==<br />
<br />
Curation/Admin<br />
* s.tweedie AT gen.cam.ac.uk<br />
<br />
Developers<br />
* emmert AT morgan.harvard.edu<br />
* p.leyland AT gen.cam.ac.uk<br />
<br />
Schema: Chado<br />
<br />
== GR (Gramene) ==<br />
<br />
<br />
* Pankaj Jaiswal<br />
* Liya Ren : ren at cshl dot edu>.<br />
<br />
== All organisms/GeneDB ==<br />
<br />
* Martin Aslett maa AT sanger DOT ac DOT uk<br />
<br />
== GeneDB ==<br />
<br />
(S.pombe, P.falciparum, L.major, T.brucei, ...)<br />
<br />
* Valerie Wood <val AT sanger DOT ac DOT uk><br />
* Martin Aslett <maa AT sanger DOT ac DOT uk><br />
<br />
== NCBI ==<br />
<br />
* ?<br />
<br />
== ''E. coli'' ==<br />
''E. coli'' has no single MOD. Several comprehensive database efforts are out there. The major ones in the US include<br />
*[http://ecocyc.org EcoCyc]. Peter Karp, SRI<br />
*[http://ecogene.org EcoGene] Kenn Rudd, Miami<br />
* ASAP. There are two ASAP sites.<br />
**[http://www.ericbrc.org/portal/eric/ ERIC BRC] John Greene, SRA. This is part of the NIAID-funded BRC program.<br />
**[http://asap.ahabs.wisc.edu/asap/home.php ASAP] Nicole Perna, Wisconsin<br />
*[http://ecolihub.org EcoliHub] Barry Wanner, Purdue. EcoliHub is supposed to help researchers find things among the many redundant ''E. coli'' sites.<br />
**[http://ecoliwiki.net EcoliWiki] is the community curation component of EcoliHub. Jim Hu, Texas A&M (jimhu at tamu.edu). Jim Hu and Debby Siegele at EcoliWiki are working with GOC on Reference Genomes.<br />
<br />
Additional information about other ''E. coli'' databases can be found at the EcoliHub website. User curation of the list of ''E. coli'' databases can be done at [http://ecoliwiki.net/colipedia/index.php/Category:E._coli_Databases EcoliWIki]<br />
<br />
== ZFIN ==<br />
<br />
* Sierra Moxon [technical contact] (staylor AT cs DOT uoregon DOT edu)<br />
* Doug Howe [curatorial contact] (dhowe AT cs DOT uoregon DOT edu)<br />
<br />
== TAIR ==<br />
<br />
* Cynthia Lee (leech AT stanford DOT edu) : technical contact<br />
* Tanya Berardini (tberardi AT acoma DOT stanford DOT edu) : curator contact<br />
<br />
== Reactome ==<br />
<br />
* gopinath AT cshl.edu<br />
* eustachi AT cshl.edu<br />
<br />
==Institute for Genome Sciences ==<br />
<br />
*Michelle Gwinn Giglio (mgiglio AT som DOT umaryland DOT edu)<br />
<br />
== J. Craig Venter Institute ==<br />
<br />
Prokaryotic<br />
*Scott Durkin (sdurkin AT jcvi DOT org)<br />
*Ramana Madupu (rmadupu AT jcvi DOT org)<br />
<br />
Eukaryotic<br />
*Linda Hannick (lhannick AT jcvi DOT org)<br />
<br />
== GrapeDB ==<br />
<br />
Genomic Research Group at CRIBI Biotechnology Centre (University of Padova, Italy)<br />
[CRIBI web site http://genomics.cribi.unipd.it]<br />
<br />
*Giorgio Valle<br />
*Nicola Vitulo<br />
*Erika Feltrin<br />
<br />
== Candida Genome Database ==<br />
*Martha Arnaud<br />
*Marek Skrzypek<br />
*Maria Costanzo<br />
<br />
candida-curator AT genome DOT stanford DOT edu</div>Mariahttps://wiki.geneontology.org/index.php?title=Register&diff=12029Register2008-03-20T17:51:13Z<p>Maria: </p>
<hr />
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[[SLC_GO_Consortium_Meeting|SLC Consortium meeting]] |<br />
[[SLC_GO_Reference_Genome_Project_Meeting|SLC Ref Genomes meeting]] | [[GO_Field_Trip|SLC field trip]] |<br />
[[Consortium_Meetings|Consortium meetings main page]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9702Meeting Notes 32008-02-20T14:49:43Z<p>Maria: /* sporulation */</p>
<hr />
<div>==Electron transport==<br />
<br />
[http://wiki.geneontology.org/index.php/Electron_transport Electron transport]<br />
<br />
<br />
==sporulation==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
'''Notes added Feb. 14, 2008 (Midori)'''<br />
<br />
(very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
sporulation GO:0030436<br><br />
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]<br />
<br />
ascospore formation GO:0030437<br><br />
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:'' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will<br />
still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
'''Debby''' 2/20/08<br />
<br />
GO:0030435 sporulation<br />
<br />
*Sexual or meiotic spores (child term of sporulation) <br />
** Ascospores (meiotically produced spores form by Ascomycetes)<br />
** Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
** Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
** Ferns<br />
<br />
*Asexual or mitotic spores (child term of sporulation) <br />
**Arthrospores (aka oidia)(Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
**Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
**Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott) <br />
**Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes) <br />
**Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
**Dictyostelium - forms spores inside fruiting bodies<br />
**Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some low G+C Gram-positive bacteria)<br />
**Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.) <br />
**Myxospore<br />
**Actinomycetes (High G+C Gram-positive bacteria that form spores)<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
Kate Dreher (TAIR)<br><br />
Tanya <br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
1. Merge ‘proteasome core complex (sensu Eukaryota)’ and ‘proteasome core complex (sensu Bacteria)’. Final term name = ‘proteasome core complex’ with improved, nice and generic definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.<br />
<br />
2. Drop (sensu Eukaryota) from ‘proteasome complex (sensu Eukaryota)’. Final term name = ‘proteasome complex’ with improved definition: A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.<br />
<br />
3. Obsolete ‘proteasome regulatory particle (sensu Bacteria)’. The current definition says: A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). The problem is that there is no ubiquitin in bacteria and they don’t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN), which we should have a new term for (see next item).<br />
<br />
4. New term: ‘proteasome –activating nucleotidase’, def: A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner.<br />
Synonym: PAN<br />
<br />
5. Drop (sensu Eukaryota) from ‘cytosolic proteasome core complex (sensu Eukaryota)’ and ‘proteasome regulatory particle (sensu Eukaryota)’. Retain current definitions and synonyms, just remove the ref to the taxon id.<br />
<br />
6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’ and improve definition from<br />
<br />
The regulatory subcomplex of a proteasome located in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A multisubunit complex located in the cytosol of a cell, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex.<br />
<br />
7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from <br />
<br />
A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A proteasome complex found in the cytosol of a cell.<br />
<br />
<br />
8. Drop (s E) from ‘proteasome regulatory particle, base subcomplex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits of the regulatory particle that directly associates with the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.<br />
<br />
9. Drop (s E) from ‘proteasome regulatory particle, lid subcomplex (sensu Eukaryota)’ and improve definition from<br />
Refers to the subunits of the regulatory particle that forms the peripheral lid, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.<br />
<br />
10. Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the outer rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex.<br />
<br />
11. Drop (s E) from ‘proteasome core complex, beta-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the inner rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex.<br />
<br />
12. The remaining terms (cytosolic blah, blah, blah) just need the (s E) dropped from their term names and the defs improved to reflect the defs of their parent terms.<br />
<br />
13. Need new term for grouping the ‘regulatory particle’ , ‘PAN’ and ‘proteasome activator complex’ (existing term with no relationship to proteasome right now. Kate and I thought of something like ‘proteasome attachment OR proteasome accessory OR proteasome accessory complex OR proteasome added stuff (ok, not the last one) with a definition something like:<br />
<br />
‘A single or multisubunit complex, which caps one or both ends of the proteasome core complex and regulates entry into or exit from the proteasome core complex.’ I hate this definition. HELP!<br />
<br />
(partial graph below, not is_a complete, you should be able to sort it out pretty easily in OBOedit)<br />
<br />
proteasome complex<br />
--[p]proteasome core complex<br />
----[p]alpha<br />
----[p]beta<br />
--[p]proteasome attachment/accessory/accessory complex (GO:new)<br />
----[i]proteasome regulatory particle<br />
------[p]base<br />
------[p]lid<br />
----[i]PAN (GO:new)<br />
----[i]proteasome activator complex<br />
<br />
The edits have been made and are being held in a branch file. The branch occurred at cvs version: $Revision: 5.631 $<br />
of gene_ontology_edit.obo. <br />
<br />
The branch is at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo.<br />
<br />
An obsoletions warning mail has been sent. <br />
<br />
<br />
Commit occurred on 15th January 2008 with addition of new terms:<br />
<br />
<br />
[Term]<br><br />
id: GO:0022624<br><br />
name: proteasome accessory complex<br><br />
namespace: cellular_component<br><br />
def: "A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex." [GOC:mtg_sensu, GOC:proteasome]<br><br />
is_a: GO:0043234 ! protein complex<br><br />
relationship: part_of GO:0000502 ! proteasome complex<br><br />
<br><br />
[Term]<br><br />
id: GO:0022625<br><br />
name: cytosolic large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005842<br><br />
alt_id: GO:0009282<br><br />
alt_id: GO:0030498<br><br />
alt_id: GO:0030872<br><br />
def: "The large subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "50S ribosomal subunit" NARROW []<br><br />
synonym: "60S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal LSU" NARROW []<br><br />
synonym: "prokaryotic large ribosomal subunit" NARROW []<br><br />
is_a: GO:0015934 ! large ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022626<br><br />
name: cytosolic ribosome<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005830<br><br />
alt_id: GO:0009281<br><br />
alt_id: GO:0030871<br><br />
def: "A ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "70S ribosome" NARROW []<br><br />
synonym: "80S ribosome" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []<br><br />
is_a: GO:0005840 ! ribosome<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
<br><br />
[Term]<br><br />
id: GO:0022627<br><br />
name: cytosolic small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005843<br><br />
alt_id: GO:0009283<br><br />
alt_id: GO:0030499<br><br />
alt_id: GO:0030873<br><br />
def: "The small subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "30S ribosomal subunit" NARROW []<br><br />
synonym: "40S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal SSU" NARROW []<br><br />
synonym: "prokaryotic small ribosomal subunit" NARROW []<br><br />
is_a: GO:0015935 ! small ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022628<br><br />
name: chloroplast large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000311 ! plastid large ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022629<br><br />
name: chloroplast small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000312 ! plastid small ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
Can we also address this at the same time? <br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=1828366&group_id=36855&atid=440764 SF1828366]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. <br>These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are<br> post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA <br>polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in <br>fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes <br>contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal <br>mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then <br>you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have <br>an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. <br>Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
Note that the 5.8S rRNA in eukaryotes corresponds to a segment of the large (23S) rRNA in prokaryotes. I have a problem with splitting the ribosomes along the sensu terms or based on the number of rRNAs, since the ontology has already divided cytosolic from organellar ribosomes. I may be misunderstanding how the ontologies are intended to be used, but it seems to me that component terms should try to avoid phylogenetic specification wherever possible, unless one wants to put the prokaryotic/eukaryotic split all the way up at the top. Otherwise, making the division for things like ribosomes can be done at too many different levels, and three vs four rRNA splits would make more sense above cytosolic vs organellar so that eukaryotic organellar would be lumped with eubacterial and archaeal, and eukaryotic cytosolic would be the outgroup. That strikes me as contrary to the "understanding the unity of life" aspect of using GO. --[[User:JimHu|JimHu]] 21:42, 22 November 2007 (PST)<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Debby Siegele (Texas A&M) speaking: Reaction center (sensu ProteoBacteria) is one of three child terms for GO:0009521: photosystem. The definitions of the other two child terms (GO:0009522: photosystem I and GO:009523: photosystem II) are specific for plants and cyanobacteria (the prokaryotic group that includes the ancestor of plant and algal chloroplasts). This is probably what led to the creation of a child term specific for the photosynthetic Proteobacteria. In addition to the two groups of photosynthetic purple bacteria that belong to the phylum Protebacteria, there are also three other groups of photosynthetic bacteria: the green sulfur bacteria, the green filamentous bacteria, and the heliobacteria. <br />
<br />
In literature that includes all types of photosynthesis reaction centers, the two types of photosystems are defined in a more inclusive way according to the nature of the electron acceptors. For example, see the following from Allen and Williams, FEBS Lett. 1998. Photosynthetic reaction centers. 438(1-2):5-9. (PMID:9821949).<br />
<br />
"Photosynthetic reaction centers can be classed into two categories based upon the nature of the electron acceptors (for a review see [R.E. Blankenship. Photosynth. Res. 33 (1992), pp. 91–111]. Purple bacteria, green filamentous bacteria, and photosystem II belong to the pheophytin-quinone type, while green sulfur bacteria, heliobacteria, and photosystem I belong to the iron-sulfur type (Fig. 1). While anoxygenic bacteria have only one photosystem, cyanobacteria and plants contain both types of photosystems. A structure for each type of reaction center has been determined by X-ray diffraction, and generalizations can be drawn from these structures since ''sequence comparisons indicate that all the reaction centers within each type are homologous'' (emphasis added)."<br />
<br />
Redefining the GO terms for photosystems I and II would allow term GO:0030090: reaction center (sensu ProteoBacteria) to be eliminated. New definitions would also illustrate the homology within each type of photosystem. Photosystems I and II both have child terms. My initial view is that that redefining the parent terms will not affect whether the child terms still follow the "true path rule", but this needs to be looked at more carefully. <br />
<br />
<br />
[[Finished Work]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9701Meeting Notes 32008-02-20T14:37:12Z<p>Maria: /* sporulation */</p>
<hr />
<div>==Electron transport==<br />
<br />
[http://wiki.geneontology.org/index.php/Electron_transport Electron transport]<br />
<br />
<br />
==sporulation==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
'''Notes added Feb. 14, 2008 (Midori)'''<br />
<br />
(very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
sporulation GO:0030436<br><br />
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]<br />
<br />
ascospore formation GO:0030437<br><br />
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:'' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will<br />
still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
'''Debby''' 2/20/08<br />
GO:0030435 sporulation<br />
<br />
*Sexual or meiotic spores<br />
<br />
** Ascospores (meiotically produced spores form by Ascomycetes)<br />
<br />
** Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
<br />
** Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
<br />
<br />
*Asexual or mitotic spores<br />
<br />
**Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
<br />
**Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
<br />
**Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)<br />
<br />
**Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes)<br />
<br />
**Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
<br />
**Dictyostelium - forms spores inside fruiting bodies<br />
<br />
**Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)<br />
<br />
**Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)<br />
<br />
**Myxospore<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
Kate Dreher (TAIR)<br><br />
Tanya <br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
1. Merge ‘proteasome core complex (sensu Eukaryota)’ and ‘proteasome core complex (sensu Bacteria)’. Final term name = ‘proteasome core complex’ with improved, nice and generic definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.<br />
<br />
2. Drop (sensu Eukaryota) from ‘proteasome complex (sensu Eukaryota)’. Final term name = ‘proteasome complex’ with improved definition: A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.<br />
<br />
3. Obsolete ‘proteasome regulatory particle (sensu Bacteria)’. The current definition says: A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). The problem is that there is no ubiquitin in bacteria and they don’t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN), which we should have a new term for (see next item).<br />
<br />
4. New term: ‘proteasome –activating nucleotidase’, def: A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner.<br />
Synonym: PAN<br />
<br />
5. Drop (sensu Eukaryota) from ‘cytosolic proteasome core complex (sensu Eukaryota)’ and ‘proteasome regulatory particle (sensu Eukaryota)’. Retain current definitions and synonyms, just remove the ref to the taxon id.<br />
<br />
6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’ and improve definition from<br />
<br />
The regulatory subcomplex of a proteasome located in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A multisubunit complex located in the cytosol of a cell, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex.<br />
<br />
7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from <br />
<br />
A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A proteasome complex found in the cytosol of a cell.<br />
<br />
<br />
8. Drop (s E) from ‘proteasome regulatory particle, base subcomplex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits of the regulatory particle that directly associates with the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.<br />
<br />
9. Drop (s E) from ‘proteasome regulatory particle, lid subcomplex (sensu Eukaryota)’ and improve definition from<br />
Refers to the subunits of the regulatory particle that forms the peripheral lid, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.<br />
<br />
10. Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the outer rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex.<br />
<br />
11. Drop (s E) from ‘proteasome core complex, beta-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the inner rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex.<br />
<br />
12. The remaining terms (cytosolic blah, blah, blah) just need the (s E) dropped from their term names and the defs improved to reflect the defs of their parent terms.<br />
<br />
13. Need new term for grouping the ‘regulatory particle’ , ‘PAN’ and ‘proteasome activator complex’ (existing term with no relationship to proteasome right now. Kate and I thought of something like ‘proteasome attachment OR proteasome accessory OR proteasome accessory complex OR proteasome added stuff (ok, not the last one) with a definition something like:<br />
<br />
‘A single or multisubunit complex, which caps one or both ends of the proteasome core complex and regulates entry into or exit from the proteasome core complex.’ I hate this definition. HELP!<br />
<br />
(partial graph below, not is_a complete, you should be able to sort it out pretty easily in OBOedit)<br />
<br />
proteasome complex<br />
--[p]proteasome core complex<br />
----[p]alpha<br />
----[p]beta<br />
--[p]proteasome attachment/accessory/accessory complex (GO:new)<br />
----[i]proteasome regulatory particle<br />
------[p]base<br />
------[p]lid<br />
----[i]PAN (GO:new)<br />
----[i]proteasome activator complex<br />
<br />
The edits have been made and are being held in a branch file. The branch occurred at cvs version: $Revision: 5.631 $<br />
of gene_ontology_edit.obo. <br />
<br />
The branch is at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo.<br />
<br />
An obsoletions warning mail has been sent. <br />
<br />
<br />
Commit occurred on 15th January 2008 with addition of new terms:<br />
<br />
<br />
[Term]<br><br />
id: GO:0022624<br><br />
name: proteasome accessory complex<br><br />
namespace: cellular_component<br><br />
def: "A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex." [GOC:mtg_sensu, GOC:proteasome]<br><br />
is_a: GO:0043234 ! protein complex<br><br />
relationship: part_of GO:0000502 ! proteasome complex<br><br />
<br><br />
[Term]<br><br />
id: GO:0022625<br><br />
name: cytosolic large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005842<br><br />
alt_id: GO:0009282<br><br />
alt_id: GO:0030498<br><br />
alt_id: GO:0030872<br><br />
def: "The large subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "50S ribosomal subunit" NARROW []<br><br />
synonym: "60S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal LSU" NARROW []<br><br />
synonym: "prokaryotic large ribosomal subunit" NARROW []<br><br />
is_a: GO:0015934 ! large ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022626<br><br />
name: cytosolic ribosome<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005830<br><br />
alt_id: GO:0009281<br><br />
alt_id: GO:0030871<br><br />
def: "A ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "70S ribosome" NARROW []<br><br />
synonym: "80S ribosome" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []<br><br />
is_a: GO:0005840 ! ribosome<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
<br><br />
[Term]<br><br />
id: GO:0022627<br><br />
name: cytosolic small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005843<br><br />
alt_id: GO:0009283<br><br />
alt_id: GO:0030499<br><br />
alt_id: GO:0030873<br><br />
def: "The small subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "30S ribosomal subunit" NARROW []<br><br />
synonym: "40S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal SSU" NARROW []<br><br />
synonym: "prokaryotic small ribosomal subunit" NARROW []<br><br />
is_a: GO:0015935 ! small ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022628<br><br />
name: chloroplast large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000311 ! plastid large ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022629<br><br />
name: chloroplast small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000312 ! plastid small ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
Can we also address this at the same time? <br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=1828366&group_id=36855&atid=440764 SF1828366]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. <br>These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are<br> post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA <br>polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in <br>fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes <br>contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal <br>mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then <br>you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have <br>an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. <br>Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
Note that the 5.8S rRNA in eukaryotes corresponds to a segment of the large (23S) rRNA in prokaryotes. I have a problem with splitting the ribosomes along the sensu terms or based on the number of rRNAs, since the ontology has already divided cytosolic from organellar ribosomes. I may be misunderstanding how the ontologies are intended to be used, but it seems to me that component terms should try to avoid phylogenetic specification wherever possible, unless one wants to put the prokaryotic/eukaryotic split all the way up at the top. Otherwise, making the division for things like ribosomes can be done at too many different levels, and three vs four rRNA splits would make more sense above cytosolic vs organellar so that eukaryotic organellar would be lumped with eubacterial and archaeal, and eukaryotic cytosolic would be the outgroup. That strikes me as contrary to the "understanding the unity of life" aspect of using GO. --[[User:JimHu|JimHu]] 21:42, 22 November 2007 (PST)<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Debby Siegele (Texas A&M) speaking: Reaction center (sensu ProteoBacteria) is one of three child terms for GO:0009521: photosystem. The definitions of the other two child terms (GO:0009522: photosystem I and GO:009523: photosystem II) are specific for plants and cyanobacteria (the prokaryotic group that includes the ancestor of plant and algal chloroplasts). This is probably what led to the creation of a child term specific for the photosynthetic Proteobacteria. In addition to the two groups of photosynthetic purple bacteria that belong to the phylum Protebacteria, there are also three other groups of photosynthetic bacteria: the green sulfur bacteria, the green filamentous bacteria, and the heliobacteria. <br />
<br />
In literature that includes all types of photosynthesis reaction centers, the two types of photosystems are defined in a more inclusive way according to the nature of the electron acceptors. For example, see the following from Allen and Williams, FEBS Lett. 1998. Photosynthetic reaction centers. 438(1-2):5-9. (PMID:9821949).<br />
<br />
"Photosynthetic reaction centers can be classed into two categories based upon the nature of the electron acceptors (for a review see [R.E. Blankenship. Photosynth. Res. 33 (1992), pp. 91–111]. Purple bacteria, green filamentous bacteria, and photosystem II belong to the pheophytin-quinone type, while green sulfur bacteria, heliobacteria, and photosystem I belong to the iron-sulfur type (Fig. 1). While anoxygenic bacteria have only one photosystem, cyanobacteria and plants contain both types of photosystems. A structure for each type of reaction center has been determined by X-ray diffraction, and generalizations can be drawn from these structures since ''sequence comparisons indicate that all the reaction centers within each type are homologous'' (emphasis added)."<br />
<br />
Redefining the GO terms for photosystems I and II would allow term GO:0030090: reaction center (sensu ProteoBacteria) to be eliminated. New definitions would also illustrate the homology within each type of photosystem. Photosystems I and II both have child terms. My initial view is that that redefining the parent terms will not affect whether the child terms still follow the "true path rule", but this needs to be looked at more carefully. <br />
<br />
<br />
[[Finished Work]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9700Meeting Notes 32008-02-20T14:29:01Z<p>Maria: /* sporulation */</p>
<hr />
<div>==Electron transport==<br />
<br />
[http://wiki.geneontology.org/index.php/Electron_transport Electron transport]<br />
<br />
<br />
==sporulation==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
'''Notes added Feb. 14, 2008 (Midori)'''<br />
<br />
(very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
sporulation GO:0030436<br><br />
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]<br />
<br />
ascospore formation GO:0030437<br><br />
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:'' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will<br />
still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
'''Debby''' 2/20/08<br />
GO:0030435 sporulation<br />
<br />
*Sexual or meiotic spores<br />
<br />
** Ascospores (meiotically produced spores form by Ascomycetes)<br />
<br />
** Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
<br />
** Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
<br />
<br />
*Asexual or mitotic spores<br />
<br />
**Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
<br />
**Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
<br />
**Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)<br />
<br />
**Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes)<br />
<br />
**Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
<br />
**Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)<br />
<br />
**Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)<br />
<br />
**Myxospore<br />
<br />
**Dictyostelium<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
Kate Dreher (TAIR)<br><br />
Tanya <br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
1. Merge ‘proteasome core complex (sensu Eukaryota)’ and ‘proteasome core complex (sensu Bacteria)’. Final term name = ‘proteasome core complex’ with improved, nice and generic definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.<br />
<br />
2. Drop (sensu Eukaryota) from ‘proteasome complex (sensu Eukaryota)’. Final term name = ‘proteasome complex’ with improved definition: A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.<br />
<br />
3. Obsolete ‘proteasome regulatory particle (sensu Bacteria)’. The current definition says: A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). The problem is that there is no ubiquitin in bacteria and they don’t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN), which we should have a new term for (see next item).<br />
<br />
4. New term: ‘proteasome –activating nucleotidase’, def: A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner.<br />
Synonym: PAN<br />
<br />
5. Drop (sensu Eukaryota) from ‘cytosolic proteasome core complex (sensu Eukaryota)’ and ‘proteasome regulatory particle (sensu Eukaryota)’. Retain current definitions and synonyms, just remove the ref to the taxon id.<br />
<br />
6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’ and improve definition from<br />
<br />
The regulatory subcomplex of a proteasome located in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A multisubunit complex located in the cytosol of a cell, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex.<br />
<br />
7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from <br />
<br />
A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A proteasome complex found in the cytosol of a cell.<br />
<br />
<br />
8. Drop (s E) from ‘proteasome regulatory particle, base subcomplex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits of the regulatory particle that directly associates with the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.<br />
<br />
9. Drop (s E) from ‘proteasome regulatory particle, lid subcomplex (sensu Eukaryota)’ and improve definition from<br />
Refers to the subunits of the regulatory particle that forms the peripheral lid, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.<br />
<br />
10. Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the outer rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex.<br />
<br />
11. Drop (s E) from ‘proteasome core complex, beta-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the inner rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex.<br />
<br />
12. The remaining terms (cytosolic blah, blah, blah) just need the (s E) dropped from their term names and the defs improved to reflect the defs of their parent terms.<br />
<br />
13. Need new term for grouping the ‘regulatory particle’ , ‘PAN’ and ‘proteasome activator complex’ (existing term with no relationship to proteasome right now. Kate and I thought of something like ‘proteasome attachment OR proteasome accessory OR proteasome accessory complex OR proteasome added stuff (ok, not the last one) with a definition something like:<br />
<br />
‘A single or multisubunit complex, which caps one or both ends of the proteasome core complex and regulates entry into or exit from the proteasome core complex.’ I hate this definition. HELP!<br />
<br />
(partial graph below, not is_a complete, you should be able to sort it out pretty easily in OBOedit)<br />
<br />
proteasome complex<br />
--[p]proteasome core complex<br />
----[p]alpha<br />
----[p]beta<br />
--[p]proteasome attachment/accessory/accessory complex (GO:new)<br />
----[i]proteasome regulatory particle<br />
------[p]base<br />
------[p]lid<br />
----[i]PAN (GO:new)<br />
----[i]proteasome activator complex<br />
<br />
The edits have been made and are being held in a branch file. The branch occurred at cvs version: $Revision: 5.631 $<br />
of gene_ontology_edit.obo. <br />
<br />
The branch is at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo.<br />
<br />
An obsoletions warning mail has been sent. <br />
<br />
<br />
Commit occurred on 15th January 2008 with addition of new terms:<br />
<br />
<br />
[Term]<br><br />
id: GO:0022624<br><br />
name: proteasome accessory complex<br><br />
namespace: cellular_component<br><br />
def: "A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex." [GOC:mtg_sensu, GOC:proteasome]<br><br />
is_a: GO:0043234 ! protein complex<br><br />
relationship: part_of GO:0000502 ! proteasome complex<br><br />
<br><br />
[Term]<br><br />
id: GO:0022625<br><br />
name: cytosolic large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005842<br><br />
alt_id: GO:0009282<br><br />
alt_id: GO:0030498<br><br />
alt_id: GO:0030872<br><br />
def: "The large subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "50S ribosomal subunit" NARROW []<br><br />
synonym: "60S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal LSU" NARROW []<br><br />
synonym: "prokaryotic large ribosomal subunit" NARROW []<br><br />
is_a: GO:0015934 ! large ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022626<br><br />
name: cytosolic ribosome<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005830<br><br />
alt_id: GO:0009281<br><br />
alt_id: GO:0030871<br><br />
def: "A ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "70S ribosome" NARROW []<br><br />
synonym: "80S ribosome" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []<br><br />
is_a: GO:0005840 ! ribosome<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
<br><br />
[Term]<br><br />
id: GO:0022627<br><br />
name: cytosolic small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005843<br><br />
alt_id: GO:0009283<br><br />
alt_id: GO:0030499<br><br />
alt_id: GO:0030873<br><br />
def: "The small subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "30S ribosomal subunit" NARROW []<br><br />
synonym: "40S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal SSU" NARROW []<br><br />
synonym: "prokaryotic small ribosomal subunit" NARROW []<br><br />
is_a: GO:0015935 ! small ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022628<br><br />
name: chloroplast large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000311 ! plastid large ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022629<br><br />
name: chloroplast small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000312 ! plastid small ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
Can we also address this at the same time? <br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=1828366&group_id=36855&atid=440764 SF1828366]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. <br>These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are<br> post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA <br>polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in <br>fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes <br>contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal <br>mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then <br>you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have <br>an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. <br>Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
Note that the 5.8S rRNA in eukaryotes corresponds to a segment of the large (23S) rRNA in prokaryotes. I have a problem with splitting the ribosomes along the sensu terms or based on the number of rRNAs, since the ontology has already divided cytosolic from organellar ribosomes. I may be misunderstanding how the ontologies are intended to be used, but it seems to me that component terms should try to avoid phylogenetic specification wherever possible, unless one wants to put the prokaryotic/eukaryotic split all the way up at the top. Otherwise, making the division for things like ribosomes can be done at too many different levels, and three vs four rRNA splits would make more sense above cytosolic vs organellar so that eukaryotic organellar would be lumped with eubacterial and archaeal, and eukaryotic cytosolic would be the outgroup. That strikes me as contrary to the "understanding the unity of life" aspect of using GO. --[[User:JimHu|JimHu]] 21:42, 22 November 2007 (PST)<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Debby Siegele (Texas A&M) speaking: Reaction center (sensu ProteoBacteria) is one of three child terms for GO:0009521: photosystem. The definitions of the other two child terms (GO:0009522: photosystem I and GO:009523: photosystem II) are specific for plants and cyanobacteria (the prokaryotic group that includes the ancestor of plant and algal chloroplasts). This is probably what led to the creation of a child term specific for the photosynthetic Proteobacteria. In addition to the two groups of photosynthetic purple bacteria that belong to the phylum Protebacteria, there are also three other groups of photosynthetic bacteria: the green sulfur bacteria, the green filamentous bacteria, and the heliobacteria. <br />
<br />
In literature that includes all types of photosynthesis reaction centers, the two types of photosystems are defined in a more inclusive way according to the nature of the electron acceptors. For example, see the following from Allen and Williams, FEBS Lett. 1998. Photosynthetic reaction centers. 438(1-2):5-9. (PMID:9821949).<br />
<br />
"Photosynthetic reaction centers can be classed into two categories based upon the nature of the electron acceptors (for a review see [R.E. Blankenship. Photosynth. Res. 33 (1992), pp. 91–111]. Purple bacteria, green filamentous bacteria, and photosystem II belong to the pheophytin-quinone type, while green sulfur bacteria, heliobacteria, and photosystem I belong to the iron-sulfur type (Fig. 1). While anoxygenic bacteria have only one photosystem, cyanobacteria and plants contain both types of photosystems. A structure for each type of reaction center has been determined by X-ray diffraction, and generalizations can be drawn from these structures since ''sequence comparisons indicate that all the reaction centers within each type are homologous'' (emphasis added)."<br />
<br />
Redefining the GO terms for photosystems I and II would allow term GO:0030090: reaction center (sensu ProteoBacteria) to be eliminated. New definitions would also illustrate the homology within each type of photosystem. Photosystems I and II both have child terms. My initial view is that that redefining the parent terms will not affect whether the child terms still follow the "true path rule", but this needs to be looked at more carefully. <br />
<br />
<br />
[[Finished Work]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9699Meeting Notes 32008-02-20T14:20:35Z<p>Maria: /* sporulation */</p>
<hr />
<div>==Electron transport==<br />
<br />
[http://wiki.geneontology.org/index.php/Electron_transport Electron transport]<br />
<br />
<br />
==sporulation==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
'''Notes added Feb. 14, 2008 (Midori)'''<br />
<br />
(very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
sporulation GO:0030436<br><br />
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]<br />
<br />
ascospore formation GO:0030437<br><br />
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:'' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will<br />
still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
'''Debby''' 2/20/08<br />
GO:0030435 sporulation<br />
<br />
Sexual or meiotic spores<br />
<br />
Ascospores<br />
<br />
<br />
Basidiospores (A haploid sexual spore formed on a basidium following the process of karyogamy and meiosis. Dr. Fungus) (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
<br />
Zygomycetes (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
<br />
<br />
Asexual or mitotic spores<br />
<br />
Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
<br />
<br />
Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
<br />
<br />
Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)<br />
<br />
<br />
Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (An asexual, non-motile, usually deciduous propagule that is not formed by cytoplasmic cleave, free-cell formation, or by conjugation. Dr. Fungus) (asexual spores formed by Ascomycetes)<br />
<br />
<br />
Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall)<br />
Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
<br />
<br />
<br />
Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)<br />
<br />
<br />
Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)<br />
<br />
<br />
Myxospore<br />
<br />
<br />
Dictyostelium<br />
<br />
<br />
Physarum?<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
Kate Dreher (TAIR)<br><br />
Tanya <br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
1. Merge ‘proteasome core complex (sensu Eukaryota)’ and ‘proteasome core complex (sensu Bacteria)’. Final term name = ‘proteasome core complex’ with improved, nice and generic definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.<br />
<br />
2. Drop (sensu Eukaryota) from ‘proteasome complex (sensu Eukaryota)’. Final term name = ‘proteasome complex’ with improved definition: A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.<br />
<br />
3. Obsolete ‘proteasome regulatory particle (sensu Bacteria)’. The current definition says: A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). The problem is that there is no ubiquitin in bacteria and they don’t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN), which we should have a new term for (see next item).<br />
<br />
4. New term: ‘proteasome –activating nucleotidase’, def: A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner.<br />
Synonym: PAN<br />
<br />
5. Drop (sensu Eukaryota) from ‘cytosolic proteasome core complex (sensu Eukaryota)’ and ‘proteasome regulatory particle (sensu Eukaryota)’. Retain current definitions and synonyms, just remove the ref to the taxon id.<br />
<br />
6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’ and improve definition from<br />
<br />
The regulatory subcomplex of a proteasome located in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A multisubunit complex located in the cytosol of a cell, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex.<br />
<br />
7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from <br />
<br />
A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A proteasome complex found in the cytosol of a cell.<br />
<br />
<br />
8. Drop (s E) from ‘proteasome regulatory particle, base subcomplex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits of the regulatory particle that directly associates with the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.<br />
<br />
9. Drop (s E) from ‘proteasome regulatory particle, lid subcomplex (sensu Eukaryota)’ and improve definition from<br />
Refers to the subunits of the regulatory particle that forms the peripheral lid, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.<br />
<br />
10. Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the outer rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex.<br />
<br />
11. Drop (s E) from ‘proteasome core complex, beta-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the inner rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex.<br />
<br />
12. The remaining terms (cytosolic blah, blah, blah) just need the (s E) dropped from their term names and the defs improved to reflect the defs of their parent terms.<br />
<br />
13. Need new term for grouping the ‘regulatory particle’ , ‘PAN’ and ‘proteasome activator complex’ (existing term with no relationship to proteasome right now. Kate and I thought of something like ‘proteasome attachment OR proteasome accessory OR proteasome accessory complex OR proteasome added stuff (ok, not the last one) with a definition something like:<br />
<br />
‘A single or multisubunit complex, which caps one or both ends of the proteasome core complex and regulates entry into or exit from the proteasome core complex.’ I hate this definition. HELP!<br />
<br />
(partial graph below, not is_a complete, you should be able to sort it out pretty easily in OBOedit)<br />
<br />
proteasome complex<br />
--[p]proteasome core complex<br />
----[p]alpha<br />
----[p]beta<br />
--[p]proteasome attachment/accessory/accessory complex (GO:new)<br />
----[i]proteasome regulatory particle<br />
------[p]base<br />
------[p]lid<br />
----[i]PAN (GO:new)<br />
----[i]proteasome activator complex<br />
<br />
The edits have been made and are being held in a branch file. The branch occurred at cvs version: $Revision: 5.631 $<br />
of gene_ontology_edit.obo. <br />
<br />
The branch is at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo.<br />
<br />
An obsoletions warning mail has been sent. <br />
<br />
<br />
Commit occurred on 15th January 2008 with addition of new terms:<br />
<br />
<br />
[Term]<br><br />
id: GO:0022624<br><br />
name: proteasome accessory complex<br><br />
namespace: cellular_component<br><br />
def: "A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex." [GOC:mtg_sensu, GOC:proteasome]<br><br />
is_a: GO:0043234 ! protein complex<br><br />
relationship: part_of GO:0000502 ! proteasome complex<br><br />
<br><br />
[Term]<br><br />
id: GO:0022625<br><br />
name: cytosolic large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005842<br><br />
alt_id: GO:0009282<br><br />
alt_id: GO:0030498<br><br />
alt_id: GO:0030872<br><br />
def: "The large subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "50S ribosomal subunit" NARROW []<br><br />
synonym: "60S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal LSU" NARROW []<br><br />
synonym: "prokaryotic large ribosomal subunit" NARROW []<br><br />
is_a: GO:0015934 ! large ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022626<br><br />
name: cytosolic ribosome<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005830<br><br />
alt_id: GO:0009281<br><br />
alt_id: GO:0030871<br><br />
def: "A ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "70S ribosome" NARROW []<br><br />
synonym: "80S ribosome" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []<br><br />
is_a: GO:0005840 ! ribosome<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
<br><br />
[Term]<br><br />
id: GO:0022627<br><br />
name: cytosolic small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005843<br><br />
alt_id: GO:0009283<br><br />
alt_id: GO:0030499<br><br />
alt_id: GO:0030873<br><br />
def: "The small subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "30S ribosomal subunit" NARROW []<br><br />
synonym: "40S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal SSU" NARROW []<br><br />
synonym: "prokaryotic small ribosomal subunit" NARROW []<br><br />
is_a: GO:0015935 ! small ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022628<br><br />
name: chloroplast large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000311 ! plastid large ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022629<br><br />
name: chloroplast small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000312 ! plastid small ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
Can we also address this at the same time? <br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=1828366&group_id=36855&atid=440764 SF1828366]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. <br>These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are<br> post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA <br>polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in <br>fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes <br>contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal <br>mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then <br>you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have <br>an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. <br>Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
Note that the 5.8S rRNA in eukaryotes corresponds to a segment of the large (23S) rRNA in prokaryotes. I have a problem with splitting the ribosomes along the sensu terms or based on the number of rRNAs, since the ontology has already divided cytosolic from organellar ribosomes. I may be misunderstanding how the ontologies are intended to be used, but it seems to me that component terms should try to avoid phylogenetic specification wherever possible, unless one wants to put the prokaryotic/eukaryotic split all the way up at the top. Otherwise, making the division for things like ribosomes can be done at too many different levels, and three vs four rRNA splits would make more sense above cytosolic vs organellar so that eukaryotic organellar would be lumped with eubacterial and archaeal, and eukaryotic cytosolic would be the outgroup. That strikes me as contrary to the "understanding the unity of life" aspect of using GO. --[[User:JimHu|JimHu]] 21:42, 22 November 2007 (PST)<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Debby Siegele (Texas A&M) speaking: Reaction center (sensu ProteoBacteria) is one of three child terms for GO:0009521: photosystem. The definitions of the other two child terms (GO:0009522: photosystem I and GO:009523: photosystem II) are specific for plants and cyanobacteria (the prokaryotic group that includes the ancestor of plant and algal chloroplasts). This is probably what led to the creation of a child term specific for the photosynthetic Proteobacteria. In addition to the two groups of photosynthetic purple bacteria that belong to the phylum Protebacteria, there are also three other groups of photosynthetic bacteria: the green sulfur bacteria, the green filamentous bacteria, and the heliobacteria. <br />
<br />
In literature that includes all types of photosynthesis reaction centers, the two types of photosystems are defined in a more inclusive way according to the nature of the electron acceptors. For example, see the following from Allen and Williams, FEBS Lett. 1998. Photosynthetic reaction centers. 438(1-2):5-9. (PMID:9821949).<br />
<br />
"Photosynthetic reaction centers can be classed into two categories based upon the nature of the electron acceptors (for a review see [R.E. Blankenship. Photosynth. Res. 33 (1992), pp. 91–111]. Purple bacteria, green filamentous bacteria, and photosystem II belong to the pheophytin-quinone type, while green sulfur bacteria, heliobacteria, and photosystem I belong to the iron-sulfur type (Fig. 1). While anoxygenic bacteria have only one photosystem, cyanobacteria and plants contain both types of photosystems. A structure for each type of reaction center has been determined by X-ray diffraction, and generalizations can be drawn from these structures since ''sequence comparisons indicate that all the reaction centers within each type are homologous'' (emphasis added)."<br />
<br />
Redefining the GO terms for photosystems I and II would allow term GO:0030090: reaction center (sensu ProteoBacteria) to be eliminated. New definitions would also illustrate the homology within each type of photosystem. Photosystems I and II both have child terms. My initial view is that that redefining the parent terms will not affect whether the child terms still follow the "true path rule", but this needs to be looked at more carefully. <br />
<br />
<br />
[[Finished Work]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9698Meeting Notes 32008-02-20T14:14:24Z<p>Maria: /* sporulation */</p>
<hr />
<div>==Electron transport==<br />
<br />
[http://wiki.geneontology.org/index.php/Electron_transport Electron transport]<br />
<br />
<br />
==sporulation==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
'''Notes added Feb. 14, 2008 (Midori)'''<br />
<br />
(very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
sporulation GO:0030436<br><br />
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]<br />
<br />
ascospore formation GO:0030437<br><br />
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:'' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will<br />
still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
'''Debby''' 2/20/08<br />
GO:0030435 sporulation<br />
Sexual or meiotic spores<br />
Ascospores<br />
<br />
Basidiospores (A haploid sexual spore formed on a basidium following the process of karyogamy and meiosis. Dr. Fungus) (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
Zygomycetes (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
<br />
Asexual or mitotic spores<br />
Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
<br />
Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
<br />
Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)<br />
<br />
Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (An asexual, non-motile, usually deciduous propagule that is not formed by cytoplasmic cleave, free-cell formation, or by conjugation. Dr. Fungus) (asexual spores formed by Ascomycetes)<br />
<br />
Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall)<br />
Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
<br />
<br />
Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)<br />
<br />
Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)<br />
<br />
Myxospore<br />
<br />
Dictyostelium<br />
<br />
Physarum?<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
Kate Dreher (TAIR)<br><br />
Tanya <br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
1. Merge ‘proteasome core complex (sensu Eukaryota)’ and ‘proteasome core complex (sensu Bacteria)’. Final term name = ‘proteasome core complex’ with improved, nice and generic definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.<br />
<br />
2. Drop (sensu Eukaryota) from ‘proteasome complex (sensu Eukaryota)’. Final term name = ‘proteasome complex’ with improved definition: A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.<br />
<br />
3. Obsolete ‘proteasome regulatory particle (sensu Bacteria)’. The current definition says: A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). The problem is that there is no ubiquitin in bacteria and they don’t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN), which we should have a new term for (see next item).<br />
<br />
4. New term: ‘proteasome –activating nucleotidase’, def: A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner.<br />
Synonym: PAN<br />
<br />
5. Drop (sensu Eukaryota) from ‘cytosolic proteasome core complex (sensu Eukaryota)’ and ‘proteasome regulatory particle (sensu Eukaryota)’. Retain current definitions and synonyms, just remove the ref to the taxon id.<br />
<br />
6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’ and improve definition from<br />
<br />
The regulatory subcomplex of a proteasome located in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A multisubunit complex located in the cytosol of a cell, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex.<br />
<br />
7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from <br />
<br />
A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A proteasome complex found in the cytosol of a cell.<br />
<br />
<br />
8. Drop (s E) from ‘proteasome regulatory particle, base subcomplex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits of the regulatory particle that directly associates with the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.<br />
<br />
9. Drop (s E) from ‘proteasome regulatory particle, lid subcomplex (sensu Eukaryota)’ and improve definition from<br />
Refers to the subunits of the regulatory particle that forms the peripheral lid, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.<br />
<br />
10. Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the outer rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex.<br />
<br />
11. Drop (s E) from ‘proteasome core complex, beta-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the inner rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex.<br />
<br />
12. The remaining terms (cytosolic blah, blah, blah) just need the (s E) dropped from their term names and the defs improved to reflect the defs of their parent terms.<br />
<br />
13. Need new term for grouping the ‘regulatory particle’ , ‘PAN’ and ‘proteasome activator complex’ (existing term with no relationship to proteasome right now. Kate and I thought of something like ‘proteasome attachment OR proteasome accessory OR proteasome accessory complex OR proteasome added stuff (ok, not the last one) with a definition something like:<br />
<br />
‘A single or multisubunit complex, which caps one or both ends of the proteasome core complex and regulates entry into or exit from the proteasome core complex.’ I hate this definition. HELP!<br />
<br />
(partial graph below, not is_a complete, you should be able to sort it out pretty easily in OBOedit)<br />
<br />
proteasome complex<br />
--[p]proteasome core complex<br />
----[p]alpha<br />
----[p]beta<br />
--[p]proteasome attachment/accessory/accessory complex (GO:new)<br />
----[i]proteasome regulatory particle<br />
------[p]base<br />
------[p]lid<br />
----[i]PAN (GO:new)<br />
----[i]proteasome activator complex<br />
<br />
The edits have been made and are being held in a branch file. The branch occurred at cvs version: $Revision: 5.631 $<br />
of gene_ontology_edit.obo. <br />
<br />
The branch is at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo.<br />
<br />
An obsoletions warning mail has been sent. <br />
<br />
<br />
Commit occurred on 15th January 2008 with addition of new terms:<br />
<br />
<br />
[Term]<br><br />
id: GO:0022624<br><br />
name: proteasome accessory complex<br><br />
namespace: cellular_component<br><br />
def: "A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex." [GOC:mtg_sensu, GOC:proteasome]<br><br />
is_a: GO:0043234 ! protein complex<br><br />
relationship: part_of GO:0000502 ! proteasome complex<br><br />
<br><br />
[Term]<br><br />
id: GO:0022625<br><br />
name: cytosolic large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005842<br><br />
alt_id: GO:0009282<br><br />
alt_id: GO:0030498<br><br />
alt_id: GO:0030872<br><br />
def: "The large subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "50S ribosomal subunit" NARROW []<br><br />
synonym: "60S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal LSU" NARROW []<br><br />
synonym: "prokaryotic large ribosomal subunit" NARROW []<br><br />
is_a: GO:0015934 ! large ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022626<br><br />
name: cytosolic ribosome<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005830<br><br />
alt_id: GO:0009281<br><br />
alt_id: GO:0030871<br><br />
def: "A ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "70S ribosome" NARROW []<br><br />
synonym: "80S ribosome" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []<br><br />
is_a: GO:0005840 ! ribosome<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
<br><br />
[Term]<br><br />
id: GO:0022627<br><br />
name: cytosolic small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005843<br><br />
alt_id: GO:0009283<br><br />
alt_id: GO:0030499<br><br />
alt_id: GO:0030873<br><br />
def: "The small subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "30S ribosomal subunit" NARROW []<br><br />
synonym: "40S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal SSU" NARROW []<br><br />
synonym: "prokaryotic small ribosomal subunit" NARROW []<br><br />
is_a: GO:0015935 ! small ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022628<br><br />
name: chloroplast large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000311 ! plastid large ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022629<br><br />
name: chloroplast small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000312 ! plastid small ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
Can we also address this at the same time? <br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=1828366&group_id=36855&atid=440764 SF1828366]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. <br>These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are<br> post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA <br>polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in <br>fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes <br>contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal <br>mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then <br>you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have <br>an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. <br>Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
Note that the 5.8S rRNA in eukaryotes corresponds to a segment of the large (23S) rRNA in prokaryotes. I have a problem with splitting the ribosomes along the sensu terms or based on the number of rRNAs, since the ontology has already divided cytosolic from organellar ribosomes. I may be misunderstanding how the ontologies are intended to be used, but it seems to me that component terms should try to avoid phylogenetic specification wherever possible, unless one wants to put the prokaryotic/eukaryotic split all the way up at the top. Otherwise, making the division for things like ribosomes can be done at too many different levels, and three vs four rRNA splits would make more sense above cytosolic vs organellar so that eukaryotic organellar would be lumped with eubacterial and archaeal, and eukaryotic cytosolic would be the outgroup. That strikes me as contrary to the "understanding the unity of life" aspect of using GO. --[[User:JimHu|JimHu]] 21:42, 22 November 2007 (PST)<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Debby Siegele (Texas A&M) speaking: Reaction center (sensu ProteoBacteria) is one of three child terms for GO:0009521: photosystem. The definitions of the other two child terms (GO:0009522: photosystem I and GO:009523: photosystem II) are specific for plants and cyanobacteria (the prokaryotic group that includes the ancestor of plant and algal chloroplasts). This is probably what led to the creation of a child term specific for the photosynthetic Proteobacteria. In addition to the two groups of photosynthetic purple bacteria that belong to the phylum Protebacteria, there are also three other groups of photosynthetic bacteria: the green sulfur bacteria, the green filamentous bacteria, and the heliobacteria. <br />
<br />
In literature that includes all types of photosynthesis reaction centers, the two types of photosystems are defined in a more inclusive way according to the nature of the electron acceptors. For example, see the following from Allen and Williams, FEBS Lett. 1998. Photosynthetic reaction centers. 438(1-2):5-9. (PMID:9821949).<br />
<br />
"Photosynthetic reaction centers can be classed into two categories based upon the nature of the electron acceptors (for a review see [R.E. Blankenship. Photosynth. Res. 33 (1992), pp. 91–111]. Purple bacteria, green filamentous bacteria, and photosystem II belong to the pheophytin-quinone type, while green sulfur bacteria, heliobacteria, and photosystem I belong to the iron-sulfur type (Fig. 1). While anoxygenic bacteria have only one photosystem, cyanobacteria and plants contain both types of photosystems. A structure for each type of reaction center has been determined by X-ray diffraction, and generalizations can be drawn from these structures since ''sequence comparisons indicate that all the reaction centers within each type are homologous'' (emphasis added)."<br />
<br />
Redefining the GO terms for photosystems I and II would allow term GO:0030090: reaction center (sensu ProteoBacteria) to be eliminated. New definitions would also illustrate the homology within each type of photosystem. Photosystems I and II both have child terms. My initial view is that that redefining the parent terms will not affect whether the child terms still follow the "true path rule", but this needs to be looked at more carefully. <br />
<br />
<br />
[[Finished Work]]</div>Mariahttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9697Meeting Notes 32008-02-20T14:09:25Z<p>Maria: /* sporulation */</p>
<hr />
<div>==Electron transport==<br />
<br />
[http://wiki.geneontology.org/index.php/Electron_transport Electron transport]<br />
<br />
<br />
==sporulation==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Michelle<br><br />
Midori<br><br />
Pascale<br><br />
Jen<br><br />
Jim Hu<br><br />
Tanya<br><br />
Debby Siegele<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features of sporulation in different species?<br><br />
<br />
'''Plan:'''<br><br />
<br />
'''Michelle speaking''' - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
Eurie is to be included in one of these calls so she can get up to speed on editing techniques. <br />
<br />
'''Debby Siegele''' (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.<br />
<br />
*GO:0030435: sporulation<br />
**GO:0030436: sporulation (sensu Bacteria)<br />
***GO:0042243: spore wall assembly (sensu Bacteria)<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
**GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic]) <br />
***GO:0030437: sporulation (sensu Fungi)<br />
****GO:0048315 : conidium formation<br />
****GO:0031321 : prospore formation<br />
****GO:0030476 : spore wall assembly (sensu Fungi)<br />
<br />
<br />
The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall. <br />
<br />
I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this. <br />
<br />
I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed. <br />
<br />
I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?<br />
<br />
A possible reorganization would be<br />
*GO:0030435: sporulation<br />
**GO:0042173: regulation of sporulation<br />
**GO:0042244: spore wall assembly<br />
** new GO term: formation of asexual spores<br />
***GO:0048315: conidium formation<br />
***new GO term: endospore formation <br />
**new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)<br />
***GO:0030437: redefined as ascospore formation<br />
<br />
In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.<br />
<br />
'''Midori''' (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)<br />
<br />
'''Notes added Feb. 14, 2008 (Midori)'''<br />
<br />
(very) rough draft of possible structure:<br />
<br />
Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!<br />
<br />
sporulation GO:0030436<br><br />
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:<br><br />
--[i] fern-type sporulation?<br><br />
--[i] moss-type sporulation?<br><br />
[i] ascospore formation GO:0030437 (renamed)<br><br />
--[p] ascospore wall formation GO:0030476 (renamed)<br><br />
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)<br><br />
[i] (a term for basidomycete sporulation) GO:new<br><br />
[i] conidium formation GO:0048315<br><br />
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")<br><br />
[i] endospore formation GO:new<br><br />
--[p] endospore wall assembly GO:new<br><br />
[i] exospore formation GO:new<br><br />
--[p] exospore wall assembly GO:new<br><br />
[i] myxospore formation GO:new<br><br />
--[p] myxospore wall v GO:new<br><br />
[i] akinete formation GO:new<br><br />
--[p] akinete wall assembly GO:new<br><br />
[p] spore wall assembly GO:0042244<br><br />
--[i] ascospore wall formation GO:0030476 (renamed)<br><br />
--[i] conidium wall assembly GO:new<br><br />
--[i] endospore wall assembly GO:new<br><br />
--[i] exospore wall assembly GO:new<br><br />
--[i] myxospore wall v GO:new<br><br />
--[i] akinete wall assembly GO:new<br><br />
[p] regulation of sporulation GO:0042173<br><br />
<br />
We can also add "xx spore wall" terms to the cellular component (CC) ontology.<br />
<br />
note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?<br />
<br />
To be made obsolete:<br><br />
- sporulation (sensu Bacteria) GO:0030436<br><br />
- spore wall assembly (sensu Bacteria) GO:0042243<br />
<br />
Some existing definitions should be rewritten. Two that I've had a stab at so far:<br />
<br />
sporulation GO:0030436<br><br />
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]<br />
<br />
ascospore formation GO:0030437<br><br />
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].<br />
<br />
Additional comments:<br />
*Reproductive sporulation<br />
**'''David:''' I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.<br />
**'''Midori:''' David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.<br />
**'''Pascale:''' I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'<br />
**'''Michelle:'' All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will<br />
still need some kind of non-reproductive sporulation term.<br />
*'''Jim:''' I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.<br />
*:'''Midori:''' I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.<br />
*'''Jim:''' The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:<br />
<br />
:http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html<br />
<br />
GO:0030435 sporulation<br />
Sexual or meiotic spores<br />
Ascospores<br />
<br />
Basidiospores (A haploid sexual spore formed on a basidium following the process of karyogamy and meiosis. Dr. Fungus) (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)<br />
Zygomycetes (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)<br />
<br />
Asexual or mitotic spores<br />
Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)<br />
<br />
Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)<br />
<br />
Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)<br />
<br />
Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (An asexual, non-motile, usually deciduous propagule that is not formed by cytoplasmic cleave, free-cell formation, or by conjugation. Dr. Fungus) (asexual spores formed by Ascomycetes)<br />
<br />
Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall)<br />
Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.<br />
<br />
<br />
Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)<br />
<br />
Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)<br />
<br />
Myxospore<br />
<br />
Dictyostelium<br />
<br />
Physarum?<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
Kate Dreher (TAIR)<br><br />
Tanya <br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
1. Merge ‘proteasome core complex (sensu Eukaryota)’ and ‘proteasome core complex (sensu Bacteria)’. Final term name = ‘proteasome core complex’ with improved, nice and generic definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.<br />
<br />
2. Drop (sensu Eukaryota) from ‘proteasome complex (sensu Eukaryota)’. Final term name = ‘proteasome complex’ with improved definition: A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.<br />
<br />
3. Obsolete ‘proteasome regulatory particle (sensu Bacteria)’. The current definition says: A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). The problem is that there is no ubiquitin in bacteria and they don’t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN), which we should have a new term for (see next item).<br />
<br />
4. New term: ‘proteasome –activating nucleotidase’, def: A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner.<br />
Synonym: PAN<br />
<br />
5. Drop (sensu Eukaryota) from ‘cytosolic proteasome core complex (sensu Eukaryota)’ and ‘proteasome regulatory particle (sensu Eukaryota)’. Retain current definitions and synonyms, just remove the ref to the taxon id.<br />
<br />
6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’ and improve definition from<br />
<br />
The regulatory subcomplex of a proteasome located in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A multisubunit complex located in the cytosol of a cell, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex.<br />
<br />
7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from <br />
<br />
A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
A proteasome complex found in the cytosol of a cell.<br />
<br />
<br />
8. Drop (s E) from ‘proteasome regulatory particle, base subcomplex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits of the regulatory particle that directly associates with the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.<br />
<br />
9. Drop (s E) from ‘proteasome regulatory particle, lid subcomplex (sensu Eukaryota)’ and improve definition from<br />
Refers to the subunits of the regulatory particle that forms the peripheral lid, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.<br />
<br />
10. Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the outer rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex.<br />
<br />
11. Drop (s E) from ‘proteasome core complex, beta-subunit complex (sensu Eukaryota)’ and improve definition from<br />
<br />
Refers to the subunits that constitute the inner rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).<br />
<br />
To<br />
<br />
Refers to the proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex.<br />
<br />
12. The remaining terms (cytosolic blah, blah, blah) just need the (s E) dropped from their term names and the defs improved to reflect the defs of their parent terms.<br />
<br />
13. Need new term for grouping the ‘regulatory particle’ , ‘PAN’ and ‘proteasome activator complex’ (existing term with no relationship to proteasome right now. Kate and I thought of something like ‘proteasome attachment OR proteasome accessory OR proteasome accessory complex OR proteasome added stuff (ok, not the last one) with a definition something like:<br />
<br />
‘A single or multisubunit complex, which caps one or both ends of the proteasome core complex and regulates entry into or exit from the proteasome core complex.’ I hate this definition. HELP!<br />
<br />
(partial graph below, not is_a complete, you should be able to sort it out pretty easily in OBOedit)<br />
<br />
proteasome complex<br />
--[p]proteasome core complex<br />
----[p]alpha<br />
----[p]beta<br />
--[p]proteasome attachment/accessory/accessory complex (GO:new)<br />
----[i]proteasome regulatory particle<br />
------[p]base<br />
------[p]lid<br />
----[i]PAN (GO:new)<br />
----[i]proteasome activator complex<br />
<br />
The edits have been made and are being held in a branch file. The branch occurred at cvs version: $Revision: 5.631 $<br />
of gene_ontology_edit.obo. <br />
<br />
The branch is at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo.<br />
<br />
An obsoletions warning mail has been sent. <br />
<br />
<br />
Commit occurred on 15th January 2008 with addition of new terms:<br />
<br />
<br />
[Term]<br><br />
id: GO:0022624<br><br />
name: proteasome accessory complex<br><br />
namespace: cellular_component<br><br />
def: "A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex." [GOC:mtg_sensu, GOC:proteasome]<br><br />
is_a: GO:0043234 ! protein complex<br><br />
relationship: part_of GO:0000502 ! proteasome complex<br><br />
<br><br />
[Term]<br><br />
id: GO:0022625<br><br />
name: cytosolic large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005842<br><br />
alt_id: GO:0009282<br><br />
alt_id: GO:0030498<br><br />
alt_id: GO:0030872<br><br />
def: "The large subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "50S ribosomal subunit" NARROW []<br><br />
synonym: "60S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal LSU" NARROW []<br><br />
synonym: "prokaryotic large ribosomal subunit" NARROW []<br><br />
is_a: GO:0015934 ! large ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022626<br><br />
name: cytosolic ribosome<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005830<br><br />
alt_id: GO:0009281<br><br />
alt_id: GO:0030871<br><br />
def: "A ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "70S ribosome" NARROW []<br><br />
synonym: "80S ribosome" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []<br><br />
is_a: GO:0005840 ! ribosome<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
<br><br />
[Term]<br><br />
id: GO:0022627<br><br />
name: cytosolic small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
alt_id: GO:0005843<br><br />
alt_id: GO:0009283<br><br />
alt_id: GO:0030499<br><br />
alt_id: GO:0030873<br><br />
def: "The small subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]<br><br />
synonym: "30S ribosomal subunit" NARROW []<br><br />
synonym: "40S ribosomal subunit" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []<br><br />
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []<br><br />
synonym: "eukaryotic ribosomal SSU" NARROW []<br><br />
synonym: "prokaryotic small ribosomal subunit" NARROW []<br><br />
is_a: GO:0015935 ! small ribosomal subunit<br><br />
is_a: GO:0044445 ! cytosolic part<br><br />
relationship: part_of GO:0022626 ! cytosolic ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022628<br><br />
name: chloroplast large ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000311 ! plastid large ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br><br />
[Term]<br><br />
id: GO:0022629<br><br />
name: chloroplast small ribosomal subunit<br><br />
namespace: cellular_component<br><br />
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br><br />
is_a: GO:0000312 ! plastid small ribosomal subunit<br><br />
relationship: part_of GO:0043253 ! chloroplast ribosome<br><br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
Can we also address this at the same time? <br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=1828366&group_id=36855&atid=440764 SF1828366]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. <br>These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are<br> post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA <br>polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in <br>fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes <br>contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal <br>mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then <br>you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have <br>an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. <br>Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
Note that the 5.8S rRNA in eukaryotes corresponds to a segment of the large (23S) rRNA in prokaryotes. I have a problem with splitting the ribosomes along the sensu terms or based on the number of rRNAs, since the ontology has already divided cytosolic from organellar ribosomes. I may be misunderstanding how the ontologies are intended to be used, but it seems to me that component terms should try to avoid phylogenetic specification wherever possible, unless one wants to put the prokaryotic/eukaryotic split all the way up at the top. Otherwise, making the division for things like ribosomes can be done at too many different levels, and three vs four rRNA splits would make more sense above cytosolic vs organellar so that eukaryotic organellar would be lumped with eubacterial and archaeal, and eukaryotic cytosolic would be the outgroup. That strikes me as contrary to the "understanding the unity of life" aspect of using GO. --[[User:JimHu|JimHu]] 21:42, 22 November 2007 (PST)<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Debby Siegele (Texas A&M) speaking: Reaction center (sensu ProteoBacteria) is one of three child terms for GO:0009521: photosystem. The definitions of the other two child terms (GO:0009522: photosystem I and GO:009523: photosystem II) are specific for plants and cyanobacteria (the prokaryotic group that includes the ancestor of plant and algal chloroplasts). This is probably what led to the creation of a child term specific for the photosynthetic Proteobacteria. In addition to the two groups of photosynthetic purple bacteria that belong to the phylum Protebacteria, there are also three other groups of photosynthetic bacteria: the green sulfur bacteria, the green filamentous bacteria, and the heliobacteria. <br />
<br />
In literature that includes all types of photosynthesis reaction centers, the two types of photosystems are defined in a more inclusive way according to the nature of the electron acceptors. For example, see the following from Allen and Williams, FEBS Lett. 1998. Photosynthetic reaction centers. 438(1-2):5-9. (PMID:9821949).<br />
<br />
"Photosynthetic reaction centers can be classed into two categories based upon the nature of the electron acceptors (for a review see [R.E. Blankenship. Photosynth. Res. 33 (1992), pp. 91–111]. Purple bacteria, green filamentous bacteria, and photosystem II belong to the pheophytin-quinone type, while green sulfur bacteria, heliobacteria, and photosystem I belong to the iron-sulfur type (Fig. 1). While anoxygenic bacteria have only one photosystem, cyanobacteria and plants contain both types of photosystems. A structure for each type of reaction center has been determined by X-ray diffraction, and generalizations can be drawn from these structures since ''sequence comparisons indicate that all the reaction centers within each type are homologous'' (emphasis added)."<br />
<br />
Redefining the GO terms for photosystems I and II would allow term GO:0030090: reaction center (sensu ProteoBacteria) to be eliminated. New definitions would also illustrate the homology within each type of photosystem. Photosystems I and II both have child terms. My initial view is that that redefining the parent terms will not affect whether the child terms still follow the "true path rule", but this needs to be looked at more carefully. <br />
<br />
<br />
[[Finished Work]]</div>Mariahttps://wiki.geneontology.org/index.php?title=GO_Field_Trip&diff=11361GO Field Trip2008-02-19T20:44:27Z<p>Maria: </p>
<hr />
<div>A field trip is planned to Antelope Island for bird watching and photography.<br />
The island is about a 45 minute drive from the university and accessed via a causeway.<br />
<br />
[[http://stateparks.utah.gov/parks/antelope-island/]] Official site<br />
<br />
[[http://en.wikipedia.org/wiki/Antelope_Island]] - wikipedia site<br />
<br />
The island has interesting geology, migrating birds pass by and there is a herd of buffalo wandering about. The colors of the island seem different to any other place. <br />
<br />
If this sounds like something you want to do, sign up so we can figure out how to get you all there.<br />
<br />
Sign up list:<br />
<br />
#Judy Blake<br />
#Susan Tweedie<br />
#Stacia Engel<br />
#Harold Drabkin</div>Mariahttps://wiki.geneontology.org/index.php?title=External_Database_Contact_Info_(Archived)&diff=11565External Database Contact Info (Archived)2008-02-19T09:58:45Z<p>Maria: </p>
<hr />
<div>Many groups associated with and outside the GOC consume the resources produced by GO, such as the gene_ontology_edit.obo file and the association files. Any major changes to these files are signaled in advanced on the gofriends list. We also would like to track the persons in charge of the technical aspects of the various different MOD databases in order to make sure they are prepared for forthcoming changes.<br />
<br />
== dictyBase ==<br />
<br />
* siddhartha-basu AT northwestern DOT edu<br />
* pgaudet AT northwestern DOT edu<br />
<br />
Schema: Chado<br />
<br />
== SGD ==<br />
<br />
* Ben Hitz ( hitz AT genome DOT stanford AT edu)<br />
* Mike Cherry (cherry AT stanford DOT edu)<br />
<br />
== RGD ==<br />
<br />
Curation<br />
* Victoria Petri vpetri at mcw dot edu<br />
* Mary Shimoyama shimoyama at mcw dot edu<br />
<br />
Technical<br />
* Alex Stoddard (astoddard at mcw dot edu)<br />
<br />
Admin<br />
* Simon Twigger simont at mcw dot edu<br />
<br />
== MGI ==<br />
<br />
* David Miers <dbm AT informatics DOT jax DOT org><br />
* Jim Kadin <jak AT informatics DOT jax DOT org><br />
<br />
==UniProtKB ==<br />
<br />
* Dan Barrel<br />
* David Binns?<br />
<br />
== WormBase ==<br />
<br />
== FlyBase ==<br />
<br />
* p.leyland AT gen.cam.ac.uk<br />
* s.tweedie AT gen.cam.ac.uk<br />
* emmer AT @morgan.harvard.edu<br />
<br />
Schema: Chado<br />
<br />
== GR (Gramene) ==<br />
<br />
* <br />
* Pankaj?<br />
<br />
== SPombe/GeneDB_* ==<br />
<br />
* Val?<br />
<br />
== NCBI ==<br />
<br />
* ?<br />
<br />
== E Coli ==<br />
<br />
* Jim Hu?<br />
<br />
== ZFIN ==<br />
<br />
* Sierra Moxon?<br />
* Doug?<br />
<br />
== TAIR ==<br />
<br />
== ==</div>Mariahttps://wiki.geneontology.org/index.php?title=Running_P-POD_orthology_tool_on_the_reference_genomes_gene_set_(Retired)&diff=11285Running P-POD orthology tool on the reference genomes gene set (Retired)2008-02-18T20:46:20Z<p>Maria: </p>
<hr />
<div>'''Input sequences'''<br />
<br />
The current plan is to start with the gp2protein files, which will be used to generate fasta files. In the future, we will use fasta files produced by the GO loading scripts after they are modified to export complete fasta files for the Ref. Genome species.<br />
<br />
Files downloaded on Feb. 7 (SGD and TAIR) and 8 (the rest, except for rat and E. coli):<br />
<br />
* Arabidopsis thaliana: gp2protein.tair.gz<br />
<br />
* Caenorhabditis elegans: gp2protein.wb.gz<br />
<br />
* Danio rerio: gp2protein.zfin.gz<br />
<br />
* Dictyostelium discoideum: gp2protein.dictyBase.gz<br />
<br />
* Drosophila melanogaster: gp2protein.fb.gz<br />
<br />
* Homo sapiens: gp2protein.human.gz<br />
<br />
* Mus musculus: gp2protein.mgi.gz<br />
<br />
* Saccharomyces cerevisiae: gp2protein.sgd.gz<br />
<br />
* Schizosaccharomyces pombe: gp2protein.genedb_spombe.gz<br />
<br />
* Rattus norvegicus: gp2protein.ncbi.rgd.gz (emailed to Kara on Feb. 4)<br />
<br />
* Escherichia coli: fasta file from Jim Hu and Anand Venkatraman<br />
<br />
* Gallus gallus: gp2protein.chicken.gz<br />
<br />
All of the input files above and the resulting fasta files can be downloaded [ftp://gen-ftp.princeton.edu/ppod/go_ref_genome/ here].<br />
<br />
Notes: <br />
<br />
- Uniprot and/or NCBI might be the source of the identifiers. Currently, not all databases provide complete sets of both, so we need to retrieve from both databases as appropriate. In the future, it would be great if all the data providers could provide both as a service to users. For our purposes, it would be useful to provide links to both resources from the web interfaces.<br />
<br />
- We have consulted with Ben at SGD, and it seems as though we can leverage the scripts that load the GO database from these files to produce the needed fasta files. This would greatly reduce redundant effort, because the existing script does essentially what we need (along with a lot more) and already has lots of data checks and such that would be very useful. Ben is currently looking at the code to see what modifications might be necessary. For the first run, we will just parse the fasta files produced here:<br />
<br />
/ftp/pub/godatabase/archive/lite/2008-02-03/go_20080203-seqdblite.fasta.gz<br />
<br />
Note: this file was incomplete.<br />
<br />
Current plan: Kara will use the gp2protein files above and re-write code to retrieve from the sequence databases as appropriate. Sequences were retrieved from NCBI or Uniprot as appropriate. Note that this is a slow process because of rules about bulk retrieval at NCBI. John Matese sped things up by getting a local version of the Uniprot database working, so retrieving those sequences, once that was implemented, was faster.<br />
<br />
'''Analysis pipeline'''<br />
<br />
The initial plan is to do all v. all BLAST, OrthoMCL, clustalW, then PHYLIP, as described here[http://ortholog.princeton.edu]. We will also make the BLAST results available separately. We can also do Jaccard Clustering to generate larger families of related sequences, if that is preferable to ortholog identification and/or is useful to have in conjunction with the ortholog families.<br />
<br />
Once we get at least the initial run finished, we will explore alternative methods and combinatorial approaches.</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10737PAMGO conference calls2008-02-15T15:24:38Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples: [[Image:regulates_relationship.doc]]<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms. <br />
<br />
See examples: [[Image:Merge_into_positive_reg.doc]]<br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Image:Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=File:Merge_into_positive_reg.doc&diff=11555File:Merge into positive reg.doc2008-02-15T15:23:06Z<p>Maria: </p>
<hr />
<div></div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10736PAMGO conference calls2008-02-15T14:50:59Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples: [[Image:regulates_relationship.doc]]<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Image:Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10735PAMGO conference calls2008-02-15T14:50:20Z<p>Maria: /* '''PAMGO Conference Call-November 15 2007''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples: [[Image:regulates_relationship.doc]]<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples:[[Image:Regulates_relationship.doc]] <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Image:Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10734PAMGO conference calls2008-02-15T14:48:23Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples: [[Image:regulates_relationship.doc]]<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples:[[Image:Regulates_relationship.doc]] <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Image:Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10733PAMGO conference calls2008-02-15T12:55:41Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples:[[Image:Regulates_relationship.doc]] <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Image:Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=File:Regulates_relationship.doc&diff=11553File:Regulates relationship.doc2008-02-15T12:53:38Z<p>Maria: </p>
<hr />
<div></div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10732PAMGO conference calls2008-02-14T21:52:16Z<p>Maria: /* '''PAMGO Conference Call-November 15 2007''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Image:Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10731PAMGO conference calls2008-02-14T20:59:14Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Image:Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10730PAMGO conference calls2008-02-14T20:58:11Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure: [[Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=File:Workshop_Brochure.pdf&diff=11552File:Workshop Brochure.pdf2008-02-14T20:57:07Z<p>Maria: </p>
<hr />
<div></div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10729PAMGO conference calls2008-02-14T20:55:43Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: [[Image:New relationship types in GO.doc]]<br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure:[[Image:Training Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=File:New_relationship_types_in_GO.doc&diff=11551File:New relationship types in GO.doc2008-02-14T20:53:21Z<p>Maria: </p>
<hr />
<div></div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10728PAMGO conference calls2008-02-14T20:47:08Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia sp<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: <br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure:[[Image:Training Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10727PAMGO conference calls2008-02-14T20:46:21Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' Update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: <br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure:[[Image:Training Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10726PAMGO conference calls2008-02-14T20:41:06Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: <br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure:[[Image:Training Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10725PAMGO conference calls2008-02-14T20:20:40Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: <br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure:[[Media:Training Workshop Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Mariahttps://wiki.geneontology.org/index.php?title=PAMGO_conference_calls&diff=10724PAMGO conference calls2008-02-14T20:17:48Z<p>Maria: /* '''PAMGO Conference Call-February 15 2008''' */</p>
<hr />
<div>=='''PAMGO Conference Call-February 15 2008'''==<br />
<br />
''' update on association files submitted to GOC''': <br />
<br />
gene_association.PAMGO_Atumefaciens.gz<br />
gene_association.PAMGO_Oomycetes.gz<br />
<br />
<br />
'''Update on association files for''':<br />
P. syringae<br />
Erwinia<br />
M. grisea<br />
<br />
<br />
'''GOC announcement: Regulation terms'''<br />
<br />
"For some time now, the GO content developers have been aware that<br />
regulatory processes are not necessarily integral to the processes (as<br />
previously indicated by the use of the 'part_of' relation) that they<br />
regulate. Nevertheless, regulatory processes have been represented as<br />
part_of the processes they regulate. We have long intended to replace<br />
these part_of relationships with a new relationship type called<br />
'regulates'. We are now in a position to make this replacement" <br />
See entire e-mail: <br />
Most of the modulation/regulation terms have a is_a relationship to parents<br />
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"<br />
See examples:<br />
<br />
<br />
'''Induction and Upregulation terms'''<br />
<br />
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive<br />
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms <br />
anyway.<br />
See examples: <br />
<br />
<br />
'''Changing wording in some host terms'''<br />
<br />
Will put a list on the wiki soon for your comments<br />
<br />
<br />
'''Mini Reviews'''<br />
<br />
<br />
'''Report'''<br />
Use of PAMGO terms by virulence community-Michelle<br />
<br />
<br />
'''PAMGO workshop July 14-16 2008'''<br />
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July<br />
We need to attract a diverse group of people this year.<br />
Download brochure:[[Training_Workshop_Brochure.pdf]]<br />
<br />
<br />
<br />
'''Others'''<br />
<br />
=='''PAMGO Conference Call-November 15 2007'''==<br />
<br />
<br />
Test set of annotations sent to Chris Mungall (GOC) [[Image:PAMGO_test_assoc.xls]]<br />
<br />
New "Properties" column in the association file<br />
<br />
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml<br />
New children codes under ISS (still under review)<br />
<br />
<br />
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree<br />
<br />
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject</div>Maria