https://wiki.geneontology.org/api.php?action=feedcontributions&user=Jclark&feedformat=atomGO Wiki - User contributions [en]2024-03-28T22:16:56ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Gohelp_rota&diff=12405Gohelp rota2008-04-10T13:18:54Z<p>Jclark: </p>
<hr />
<div>*'''Jennifer:''' 10th March - 16th March<br />
*'''Emily:''' 17th March - 23rd March<br />
*'''David:''' 24th March - 30th March<br />
*'''Jane:''' 31st March - 6th April<br />
*'''Kimberly:''' 7th April - 13th April<br />
*'''Midori:''' 14th April - 20th April<br />
*'''Amelia:''' 21st April - 27th April<br />
*'''Tanya:''' 28th April - 4th May<br />
*'''Eurie:''' 5th May - 11th May<br />
*'''Jennifer:''' 12th May - 19th May<br />
*'''Rachael:''' 20th May -</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Muscle_biology-_Muscle_Meeting_Minutes&diff=12404Muscle biology- Muscle Meeting Minutes2008-04-10T12:51:22Z<p>Jclark: </p>
<hr />
<div>[[5th February 2008]]<br />
<br />
[[Muscle 4th March 2008]]<br />
<br />
<br />
==11th March, 2008==<br />
<br />
Participants: Erika Feltrin, Jennifer Deegan,<br />
<br />
We discussed plans for publication of the muscle paper.<br />
<br />
GMC Medical Genomics has suggested that we should send the paper as a research article, and that they should be able to publish it as a communication, if we attach the email from the editor.<br />
<br />
Erika has the latest version of the paper, with Judy's changes, not yet incorporated, and the template from the journal.<br />
<br />
We considered who the authors on the paper should be. Erika suggests:<br />
<br />
Erika Feltrin, Jennifer Deegan, Giorgio Valle, and the Muscle Biology GO Working Group. This would mirror the way the authors were set up on the OBO-Edit paper and seems to include everyone appropriately.<br />
<br />
We need to acknowledge the Telethon and NIH funding. Do we also need to acknowledge EMBL funding?<br />
<br />
For the journal we need to find four peer reviewers who have not co-published with the authors on the paper, but who are interested, and in the field.<br />
<br />
We need to write a conclusion section, but it can be very short.<br />
<br />
During the meeting we worked through the introduction of our current draft, incorporated Judy's changes, and made lots of further improvements. Erika is going to paste the text into the BMC Medical Genomics template before tomorrow when we meet again at 11am.<br />
<br />
<br />
==12th and 13th March, 2008== <br />
<br />
Participants: Erika Feltrin and Jennifer Deegan.<br />
<br />
We redrafted the remainder of the paper to the structure required by BMC Medical Genomics. We now need to double-check the reference format, the grant acknowledgment and some other small details.<br />
<br />
==14th March, 2008== <br />
<br />
Participants: Erika Feltrin and Jennifer Deegan.<br />
<br />
We put the finishing touches to our draft and it is now ready to be sent to the GO list. <br />
<br />
[The mail to the GO list was sent later on the same day.]<br />
<br />
<br />
==26th/27th March, 10am - 11.30am==<br />
<br />
Participants: Erika Feltrin and Jennifer Deegan.<br />
<br />
We made further revisions to the manuscript. <br />
<br />
To do: Jen to make a screenshot to add as a figure.<br />
<br />
==9th April 2008==<br />
<br />
Erika and I had a rehearsal for her viva.</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Steve_Oliver%27s_Transport_Group&diff=12403Steve Oliver's Transport Group2008-04-10T12:50:31Z<p>Jclark: </p>
<hr />
<div>Steve Oliver, who I met at the EuroFung Aspergillus annotation meeting, is interested to initiate a GO transport meeting to look at some aspects of function and process. He is now based in Cambridge and we have agreed that now is a good time for us to look at doing the work. I am in contact to try to figure out a good time to visit. <br />
<br />
<br />
==18th January 2008==<br />
<br />
I visited Steve Oliver at the Biochemistry Department (new building) on Tennis Court Road. I gave him a tour of the new high level terms and he was impressed with what we have done so far. We talked about how annotation should work where drugs are being transported by transporters that normally transport non-drug solutes and I explained about our plan to structure the graph along chemical structure lines, rather than have people annotate to 'xenobiotic transporter activity' or 'drug transporter activity'. He said that would work best for them too. He has a colleague called Paul Dobson who has recently completed a review of the transporters and Steve is wondering if Paul would be prepared to work with us to update the terms, as his knowledge is now completely up to date. He is going to ask on Monday 20th when he visits him in Manchester. There is another colleague called Andre Goffeau who might also help. I have searched for Paul Dobson's review but it doesn't show up in searches so I don't think it can be in print yet. It is in one of the nature review journals.<br />
<br />
==28th March 2008==<br />
<br />
Steve Oliver wrote to say that he has spoken to Paul Dobson (paul.dobson AT manchester.ac.uk), the post-doc in Manchester to discuss our ideas. <br />
<br />
He is also interested in possibly holding the next EuroFung annotation jamboree at the EBI. I wrote back to say that all of this sounded excellent, and would he like some information on costings for the jamboree. I explained about all the infrastructure that we have set up to support this kind of thing.<br />
<br />
==10th April 2008==<br />
<br />
I am now in correspondance with Paul Dobson and am reading his review paper on drug transport. 'Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule?' Paul is a bioinformatician who has been reading a huge number of papers to write this review and so is very up to date. He is currently on a transition between grants, but is going to get back to me soon.</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12402Managers 9April082008-04-10T12:17:37Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
<br />
'''JGI Collaboration'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not bring in predicted annotations. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
'''Web Presence group'''<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
*General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
*Lack of biologists on the group means their needs are not represented. <br><br />
*Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
*Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
'''Conclusion:''' this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
['''Discussion between Jen and Jane after call:'''<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>She would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalized:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [[SWUG:Quality_Control|software QC]]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[[Derived_files_in_CVS]].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12401Managers 9April082008-04-10T12:13:45Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
<br />
'''JGI Collaboration'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
'''Web Presence group'''<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
*General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
*Lack of biologists on the group means their needs are not represented. <br><br />
*Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
*Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
'''Conclusion:''' this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
['''Discussion between Jen and Jane after call:'''<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>She would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalized:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [[SWUG:Quality_Control|software QC]]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[[Derived_files_in_CVS]].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12400Managers 9April082008-04-10T11:53:30Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
<br />
'''JGI Collaboration'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
'''Web Presence group'''<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
*General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
*Lack of biologists on the group means their needs are not represented. <br><br />
*Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
*Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
'''Conclusion:''' this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
['''Discussion between Jane and Jane after call:'''<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>She would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalized:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [[SWUG:Quality_Control|software QC]]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[[Derived_files_in_CVS]].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12399Managers 9April082008-04-10T11:50:21Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
<br />
'''JGI Collaboration'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
'''Web Presence group'''<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
*General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
*Lack of biologists on the group means their needs are not represented. <br><br />
*Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
*Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
'''Conclusion:''' this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
['''Discussion between Jane and Jane after call:'''<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>She would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalised:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [[SWUG:Quality_Control|software QC]]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[[Derived_files_in_CVS]].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12398Managers 9April082008-04-10T11:49:49Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
'''JGI'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
'''Web Presence group'''<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
*General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
*Lack of biologists on the group means their needs are not represented. <br><br />
*Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
*Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
'''Conclusion:''' this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
['''Discussion between Jane and Jane after call:'''<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>She would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalised:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [[SWUG:Quality_Control|software QC]]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[[Derived_files_in_CVS]].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12397Managers 9April082008-04-10T11:48:57Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
'''JGI'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
'''Web Presence group'''<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
*General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
*Lack of biologists on the group means their needs are not represented. <br><br />
*Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
*Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
'''Conclusion:''' this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
['''Discussion between Jane and Jane after call:'''<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>Should would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalised:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [[SWUG:Quality_Control|software QC]]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[[Derived_files_in_CVS]].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12396Managers 9April082008-04-10T11:47:47Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
'''JGI'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
'''Web Presence group'''<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
*General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
*Lack of biologists on the group means their needs are not represented. <br><br />
*Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
*Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
'''Conclusion:''' this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
['''Discussion between Jane and Jane after call:'''<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>Should would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
* Instituted [[SWUG:Quality_Control|software QC]] principles<br />
* OBO-Edit text mining plugin<br />
*[[Derived_files_in_CVS]] - can everyone check and make sure this is complete<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalised:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [link?]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[http://wiki.geneontology.org/index.php/Derivedfilesincvs?].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12395Managers 9April082008-04-10T11:46:46Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
'''JGI'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
Lack of biologists on the group means their needs are not represented. <br><br />
Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
Conclusion: this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
[Discussion between Jane and Jane after call:<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>Should would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
* Instituted [[SWUG:Quality_Control|software QC]] principles<br />
* OBO-Edit text mining plugin<br />
*[[Derived_files_in_CVS]] - can everyone check and make sure this is complete<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalised:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [link?]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[http://wiki.geneontology.org/index.php/Derivedfilesincvs?].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12394Managers 9April082008-04-10T11:46:30Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
'''JGI'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
Lack of biologists on the group means their needs are not represented. <br><br />
Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
Conclusion: this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
[Discussion between Jane and Jane after call:<br><br />
Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. <br>Should would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
* Instituted [[SWUG:Quality_Control|software QC]] principles<br />
* OBO-Edit text mining plugin<br />
*[[Derived_files_in_CVS]] - can everyone check and make sure this is complete<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalised:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [link?]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[http://wiki.geneontology.org/index.php/Derivedfilesincvs?].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12393Managers 9April082008-04-10T11:45:48Z<p>Jclark: </p>
<hr />
<div>GO Managers, Weds. April 9th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM GMT<br><br />
<br />
Agenda/chair: Pascale<br><br />
<br />
Minutes: Jennifer<br />
<br />
Present: Midori Harris, Pascale Gaudet, Judy Blake, Suzanna Lewis, Chris Mungall, Jane Lomax, Jennifer Deegan, David Hill. <br />
<br />
<br />
==Action Items==<br />
<br />
Review Action Items from previous meeting<br><br />
<br />
'''All:''' Check list of database contacts and make any additions needed. http://wiki.geneontology.org/index.php/External_Database_Contact_Info. Chris to email GO List.<br />
DONE<br />
<br />
'''cvs rearrangement:'''<br />
* ACTION ITEM: Mike/Chris need to agree on the date to put scripts in place. Put scripts in place. DONE <br />
* Chris will send a pre-announcement to go-friends mailing list to announce the new file DONE<br />
<br />
'''Reference Genome group:''' Decide on QC procedures, frequency, etc.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Determine protocol for making ISS annotations.<br />
[In the Ref genomes meeting agenda]<br />
<br />
'''Reference Genome group:''' Try WebEx "raise hand" feature for next conf call.<br />
Pascale will put that in the agenda for ref genomes meeting<br />
[DONE - failed...]<br />
<br />
==Ontology Development==<br />
'''Regulates loaded in AmiGO?'''<br><br />
DONE - regulates fully implemented. <br />
<br />
'''Sensu'''<br><br />
Removal of sensu endings and proper definition and naming of terms now finished. <br><br />
'''Signaling overhaul started.''' <br><br />
Initial ideas for structure at:<br><br />
http://wiki.geneontology.org/index.php/Signaling_ontology_structure_documentation<br><br />
Comments welcomed. <br />
<br />
'''Lung development'''<br> overhaul about to recommence<br><br />
'''Lipoprotein terms for reactome and UCL'''<br> Now added.<br> <br />
'''Various content items added to salt lake city agenda.'''<br><br />
<br />
'''Quality control''' <br><br />
Page on wiki: to collect all quality control projects:<br><br />
[link?] <br />
<br />
==Outreach/User Advocacy==<br />
<br />
'''ISSN'''<br><br />
Applying for ISSN for the newsletter..<br />
<br />
===advocacy/outreach topics for SLC:===<br />
<br />
'''Reactome'''<br />
Collaboration with Reactome to be discussed.<br><br />
Jen: Emily has this in hand and is working with Esther Schmidt to make sure the necessary changes are made. The work is not yet ready but this is because Esther has been busy with other priorities. <br><br />
'''JGI'''<br><br />
<br />
'''Groups producing predictions'''<br>Does it make sense to bring in prediction annotations when they go stale within a year?<br><br />
(Current policy is that we do not do this. - Should this change?) <br><br />
<br />
Things generally to consider:<br />
*annotation assistance<br />
*software needs<br />
*web presence<br />
*gohelp<br />
etc...<br />
<br />
Jane: We need to figure out how to prioritize. <br />
<br />
Suzi's priority list:<br />
<br />
*gohelp<br />
*web presence<br />
*reatome etc<br />
*nurturing other new groups<br />
* bringing in IEAs.<br />
<br />
Should Jane and Jen work with web presence to make release more co-ordinated and ensure that user needs are taken into account?<br />
<br />
General agreement that the web presence group needs more co-ordination. No clear plan on who should deliver that. <br><br />
Lack of biologists on the group means their needs are not represented. <br><br />
Web presence calls seem to be all about technical issues, so biologists who do join quickly drop out again. These calls should not be dominated by technical issues.<br> <br />
Concern from Jen and Jane that any time they spend managing web presence is time that they do not spend on ontology content. <br><br />
<br />
Conclusion: this group needs better co-ordination, but it's not clear who should provide that. <br />
<br />
[Discussion between Jane and Jane after call: Jane could perhaps spend half a day a week giving the biologist viewpoint and being release manager when needed. Should would not be technical manager though, as that could come from the software side.]<br />
<br />
==Software==<br />
<br />
* Instituted [[SWUG:Quality_Control|software QC]] principles<br />
* OBO-Edit text mining plugin<br />
*[[Derived_files_in_CVS]] - can everyone check and make sure this is complete<br />
<br />
'''cvs'''<br><br />
The cvs rearrangement is now all in place.<br><br />
Encouraging people to use new file paths. <br />
<br />
'''Reaching users'''<br><br />
Question: Do we have a list beyond go-friends for our major users? e.g. uniprot etc.<br><br />
Surely this is what go-friends is for?<br><br />
Do we need an RSS feed?<br><br />
Perhaps have something on download pages?<br />
<br />
'''QC'''<br><br />
Quality control has been formalised:<br><br />
Eliminating a bug that causes web search engines to hammer database. <br><br />
Could have caught this with automated testing. Now improving this testing framework. <br><br />
Comments on the wiki page welcomed [link?]. <br><br />
<br />
'''Derived Files'''<br><br />
Software group want to collect in file system or on wiki list of derived files in cvs.<br><br />
i.e. which files are derived from other files via a script that is run on a cron job, and who is responsible for those scripts?<br><br />
Need to have a list of these on a wiki page:<br><br />
page:<br><br />
[http://wiki.geneontology.org/index.php/Derivedfilesincvs?].<br />
<br />
'''New tracker system:'''<br><br />
A demo is now available for people to try. [link?]<br />
<br />
'''AmiGO1.6'''<br><br />
Seth sent a link for people to test AmiGO 1.6. Sent to web presence working group. Needs feedback. <br />
<br />
'''Bulk Loading'''<br><br />
Ben written bulk loading script to make loads happen quicker. <br><br />
<br />
'''OBO-Edit'''<br><br />
Demo of OBO-Edit plugin from Michael Schroeder's group. Michael is going to do some more polishing and send out a version to let people try. It is a text mining tool. We will set aside some time to demo it at the meeting. We will try to do it at a time where we can reach Michael if we have questions. Michael should come to Nomi or Chris to get this into the main source tree of OBO-Edit. David says a separate plugin may be best. So people can add it on if they want it. Will be very useful if it works well. We should have a go at it. <br />
<br />
'''Goose'''<br><br />
Is Goose safe against rogue SQL? Yes it can only bring down an internal database in Berkeley. It would not bring down AmiGO. <br />
<br />
==Reference Genome==<br />
*Monthly call was yesterday; not too many people<br />
*orthology determination (P-POD) is 'on schedule'<br />
*curation tool for reference genomes is progressing<br />
*Suzi, Judy, Michael made a nice 'annotation pipeline' document, available at: http://wiki.geneontology.org/index.php/Annotation_pipeline<br />
*Annotators liked the document<br />
*we'll meet next week to discuss it<br />
*Pascale is having a hard time making people 'complete' the annotations; some people want to wait for the 'pipeline' to be in place, but she is not sure how different it will be<br />
<br />
In MGI they have an internal wiki so they can co-ordinate who is doing which reference genome gene. <br><br />
Maybe on wiki just post list of genes and people can mark if they are done. This is until the database is all ready to hold the ref genome stats. <br />
Database may be ready in a month. <br />
<br />
'''Programmers working on annotation tool.'''<br><br />
All on schedule.<br><br />
BLAST part done.<br><br />
Already preliminary version ready. <br />
<br />
<br />
==Meetings==<br />
<br />
'''GO meeting agenda'''<br><br />
Some discussion of how best to arrange the agenda.<br><br />
Reference genome section should just be a report from ref genome meeting, so no lengthy discussion needed. <br><br />
<br />
'''General point from Suzi:'''<br><br />
We need to know who is responsible for what across the board. <br><br />
Could add to agenda 'is there anything where we are missing a responsible person?' <br><br />
We should have no duplication of effort, and no areas of work that are without a responsible person. <br><br />
<br />
'''Agenda plan'''<br><br />
For all topics, managers should look at their individual areas on the agenda and adjust things to make sure the most importnat points are discussed in an appropriate order. Go the wiki and make adjustments. <br />
<br />
*[[SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda| Reference genomes meeting agenda]]<br />
<br />
==Collaborations and Interactions==<br />
<br />
==Operations and Procedures==<br />
<br />
== Staffing and Personnel ==<br />
<br />
== Budget issues ==<br />
<br />
<br />
== Publications ==<br />
* ref genome paper... Pascale would like to start working on that again<br />
<br />
== Other issues ==<br />
<br />
<br />
[[GO_Managers_conference_call_minutes|Back to minutes list]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Managers_9April08&diff=12227Managers 9April082008-04-03T13:04:30Z<p>Jclark: New page: Agenda item (Jen): Do Jane and I need to do managers' reports on outreach and advocacy for the consortium meeting? This have been very quiet for both groups lately and time is quite tig...</p>
<hr />
<div><br />
<br />
<br />
Agenda item (Jen): Do Jane and I need to do managers' reports on outreach and advocacy for the consortium meeting? This have been very quiet for both groups lately and time is quite tight at the meeting.</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Project_stand_up_meetings&diff=12226Project stand up meetings2008-04-03T13:03:12Z<p>Jclark: </p>
<hr />
<div>==2008==<br />
*[[managers_9April|April 9]]<br />
*[[managers_26March|March 26]]<br />
*[[managers_12March|March 12]]<br />
*[[managers_27_February|February 27]]<br />
*[[managers_13Feb08|February 13]]<br />
*[[managers_30Jan08|January 30]]<br />
*[[managers_16Jan08|January 16]]<br />
*[[managers_2Jan08|January 2]]<br />
<br />
==2007==<br />
*[[managers_19Dec07|December 19]]<br />
*[[managers_21Nov07|November 21]]<br />
*[[managers_7Nov07|November 7]]<br />
*[[managers_24Oct07|October 24]]<br />
*[[managers_10Oct07|October 10]]<br />
*[[managers_12Sept07|September 12]]<br />
*[[managers_29Aug07|August 29]]<br />
*[[managers_15Aug07|August 15]]<br />
*[[managers_1August07|August 1]]<br />
*[[managers_18July07|July 18]]<br />
*[[managers_20Jun07|June 20]]<br />
*[[managers_6Jun07|June 6]]<br />
*[[managers_23May07|May 23]]<br />
*[[managers_9May07|May 9]]<br />
*[[managers_25Apr07|April 27]]<br />
*[[managers_11Apr07|April 11]]<br />
*[[managers_28Mar07|March 28]]<br />
*[[managers_14Mar07|March 14]]<br />
*[[managers_28Feb07|February 28]]<br />
*[[managers_14Feb07|February 14]]<br />
*[[managers_31Jan07|January 31]]<br />
*[[managers_17Jan07|January 17]]<br />
*[[managers_3Jan07|January 3]]<br />
<br />
==2006==<br />
*[[managers_20Dec06|December 20]]<br />
*[[managers_29Nov06|November 29]]<br />
*[[managers_8Nov06|November 8]]<br />
*[[managers_25Oct06|October 25]]<br />
*[[managers_11Oct06|October 11]]<br />
*[[managers_27Sept06|September 27]]<br />
*[[managers_13Sept06|September 13]]<br />
*[[managers_30Aug06|August 30]]<br />
*[[managers_16Aug06|August 16]]<br />
*[[managers_19July06|July 19]]<br />
*[[managers_5July06|July 5]]<br />
*[[managers_21June06|June 21]]<br />
*[[managers_2June06|June 2]]<br />
*[[managers_5May06|May 5]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Gohelp_rota&diff=12225Gohelp rota2008-04-03T13:01:24Z<p>Jclark: </p>
<hr />
<div>*'''Jennifer:''' 10th March - 16th March<br />
*'''Emily:''' 17th March - 23rd March<br />
*'''David:''' 24th March - 30th March<br />
*'''Jane:''' 31st March - 6th April<br />
*'''Kimberly:''' 7th April - 13th April<br />
*'''Midori:''' 14th April - 20th April<br />
*'''Amelia:''' 21st April - 27th April<br />
*'''Tanya:''' 28th April - 4th May<br />
*'''Eurie:''' 5th May - 11th May<br />
*'''Jennifer:''' 12th May - 19th May</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Muscle_biology-_Muscle_Meeting_Minutes&diff=12144Muscle biology- Muscle Meeting Minutes2008-03-27T11:49:03Z<p>Jclark: </p>
<hr />
<div>[[5th February 2008]]<br />
<br />
[[Muscle 4th March 2008]]<br />
<br />
<br />
==11th March, 2008==<br />
<br />
Participants: Erika Feltrin, Jennifer Deegan,<br />
<br />
We discussed plans for publication of the muscle paper.<br />
<br />
GMC Medical Genomics has suggested that we should send the paper as a research article, and that they should be able to publish it as a communication, if we attach the email from the editor.<br />
<br />
Erika has the latest version of the paper, with Judy's changes, not yet incorporated, and the template from the journal.<br />
<br />
We considered who the authors on the paper should be. Erika suggests:<br />
<br />
Erika Feltrin, Jennifer Deegan, Giorgio Valle, and the Muscle Biology GO Working Group. This would mirror the way the authors were set up on the OBO-Edit paper and seems to include everyone appropriately.<br />
<br />
We need to acknowledge the Telethon and NIH funding. Do we also need to acknowledge EMBL funding?<br />
<br />
For the journal we need to find four peer reviewers who have not co-published with the authors on the paper, but who are interested, and in the field.<br />
<br />
We need to write a conclusion section, but it can be very short.<br />
<br />
During the meeting we worked through the introduction of our current draft, incorporated Judy's changes, and made lots of further improvements. Erika is going to paste the text into the BMC Medical Genomics template before tomorrow when we meet again at 11am.<br />
<br />
<br />
==12th and 13th March, 2008== <br />
<br />
Participants: Erika Feltrin and Jennifer Deegan.<br />
<br />
We redrafted the remainder of the paper to the structure required by BMC Medical Genomics. We now need to double-check the reference format, the grant acknowledgment and some other small details.<br />
<br />
==14th March, 2008== <br />
<br />
Participants: Erika Feltrin and Jennifer Deegan.<br />
<br />
We put the finishing touches to our draft and it is now ready to be sent to the GO list. <br />
<br />
[The mail to the GO list was sent later on the same day.]<br />
<br />
<br />
==26th/27th March, 10am - 11.30am==<br />
<br />
Participants: Erika Feltrin and Jennifer Deegan.<br />
<br />
We made further revisions to the manuscript. <br />
<br />
To do: Jen to make a screenshot to add as a figure.</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12118Signaling ontology structure documentation2008-03-26T17:27:50Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
[i]regulation of signaling<br />
---[i]process mediating persistance of signaling effect after signal has gone<br />
---[i]process mediating response to signal molecule gradient<br />
---[i]process of adjustment of sensitivity to signal<br />
---[i]process of linking signals to alter response<br />
------[i]scaffold protein-mediated regulation of signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12117Signaling ontology structure documentation2008-03-26T17:27:31Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
[i]regulation of signaling<br />
---[i]process mediating persistance of signaling effect after signal has gone<br />
---[i]process mediating response to signal molecule gradient<br />
---[i]process of adjustment of sensitivity to signal<br />
---[i]process of linking signals to alter response<br />
------[i]scaffold protein-mediated regulation of signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12116Signaling ontology structure documentation2008-03-26T17:27:10Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
[i]regulation of signaling<br />
---[i]process mediating persistance of signaling effect after signal has gone<br />
---[i]process mediating response to signal molecule gradient<br />
---[i]process of adjustment of sensitivity to signal<br />
---[i]process of linking signals to alter response<br />
------[i]scaffold protein-mediated regulation of signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12115Signaling ontology structure documentation2008-03-26T17:26:58Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
[i]regulation of signaling<br />
---[i]process mediating persistance of signaling effect after signal has gone<br />
---[i]process mediating response to signal molecule gradient<br />
---[i]process of adjustment of sensitivity to signal<br />
---[i]process of linking signals to alter response<br />
------[i]scaffold protein-mediated regulation of signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12113Signaling ontology structure documentation2008-03-26T17:17:14Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
---[i]intracellular signaling<br />
------[i]large intracellular molecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12112Signaling ontology structure documentation2008-03-26T17:16:55Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
---[i]intracellular signaling<br />
------[i]large intracellular molecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12111Signaling ontology structure documentation2008-03-26T17:15:47Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12110Signaling ontology structure documentation2008-03-26T17:15:20Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]signaling systems grouped by location of the signal molecule<br />
---[i]cell surface receptor protein-mediated signaling<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling<br />
<br />
//These are a bit of a mouthful.<br />
<br />
[i]cell surface receptor protein-mediated signaling<br />
---[i]ion-channel linked cell surface receptor protein-mediated signaling<br />
---[i]G-Protein linked cell surface receptor protein-mediated signaling<br />
---[i]enzyme linked cell surface receptor protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12109Signaling ontology structure documentation2008-03-26T17:07:31Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small molecules are also going to be difficult. <br />
<br />
[i]large intracellular molecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12108Signaling ontology structure documentation2008-03-26T17:07:14Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small molecules are also going to be difficult. <br />
<br />
[i]large intracellular molecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12107Signaling ontology structure documentation2008-03-26T17:06:59Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small molecules are also going to be difficult. <br />
<br />
[i]large intracellular molecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12106Signaling ontology structure documentation2008-03-26T17:06:25Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
---[i]intracellular signaling<br />
------[i]large intracellular mloecule-mediated signaling<br />
---[i]intercellular signaling<br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
---[i]signaling to control gene expression<br />
<br />
<br />
[i]long distance signaling<br />
[i]short distance signaling<br />
<br />
[i]molecular switch-like signaling<br />
---[i]phosphoylation/dephosphorylation-mediated signaling<br />
---[i]GTP-binding protein-mediated signaling<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response<br />
<br />
<br />
//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals. <br />
<br />
[i]long distance signaling<br />
---[i]long distance hormone-mediated signaling<br />
---[i]long distance nervous system-mediated signaling<br />
<br />
[i]short distance signaling<br />
---[i]local mediators (paracrine signaling)<br />
<br />
//large and small moleculaes are also going to be difficult. <br />
<br />
[i]large intracellular mloecule-mediated signaling<br />
---[i]relay protein-mediated signaling<br />
---[i]messenger protein-mediated signaling<br />
---[i]adaptor protein-mediated signaling<br />
---[i]amplifier protein-mediated signaling<br />
---[i]transducer protein-mediated signaling<br />
---[i]bifurcation protein-mediated signaling<br />
---[i]integrator protein-mediated signaling<br />
---[i]latent gene regulatory protein-mediated signaling</div>Jclarkhttps://wiki.geneontology.org/index.php?title=SLC_GO_Consortium_Meeting&diff=12100SLC GO Consortium Meeting2008-03-26T15:58:58Z<p>Jclark: </p>
<hr />
<div>== Venue ==<br />
<br />
==='''Meeting Room'''===<br />
*The Meeting will be held in the Salt Lake City Library, Conference Room 4<br />
*210 East 400 South, SLC UT 84111<br />
*http://www.slcpl.lib.ut.us/locations.jsp?parent_id=8&page_id=20<br />
<br />
*Conference Room 4 is the large conference room on the 4th floor, located behind the front desk to the right.<br />
*We are not allowed to put posters up to direct you, but if you get lost, the library staff will point you in the right direction.<br />
<br />
==='''Dates:'''=== <br />
*April 22-23, 2008 <br />
*We will be providing lunch on the 22nd<br />
*The meeting ends at lunchtime on the 23rd.<br />
*Dinner will be held on Tuesday 22nd April at [http://www.cannellas.com/ Cannellas]. The reservation is for 6.30, and it is located one block South from the library.<br />
<br />
==='''Cost'''===<br />
* $50.00; Receipt will be provided at registration. Checks should be made payable to the Department of Human Genetics. The address if needed for the check is: Eccles Institute of Human Genetics, Building 533, University of Utah, 15 North 2030 East, Salt Lake City, Utah. 84112.<br />
* Dinner: cost TBD; we are looking for a sponsor<br />
* You are responsible for your lodging costs<br />
<br />
==='''Lodging:'''===<br />
*The [http://www.guesthouse.utah.edu/ugh/information.htm University GuestHouse]is a good place to stay as it is a short walk to HSEB. If you are also attending the Reference Genome Meeting, it is a small walk from the that venue, and a tram ride from the library - door to door.<br />
*Please make reservations early as it is a popular place and there will be extra people in town for the marathon.<br />
<br />
*If you need to make other arrangements let me know (Karen E) and I will find a different hotel. <br />
*The [http://marriott79-px.trvlclick.com/hotels/travel/slcup-salt-lake-city-marriott-university-park/ | University_Marriott] at the university is a cab ride from both venues.<br />
<br />
*There are many hotels downtown with reasonable rates such as the Little America and the Red Lion.<br />
*The [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/| Downtown_Marriott] within walking distance of the library, but it is $259 per night!<br />
*To book a taxi from the library to the airport: 801 521 2100<br />
<br />
== Registration ==<br />
Please [[http://gocwiki.geneontology.org/index.php/Register#Registration_for_April_2008_GO_Meetings_at_University_of_Utah.2C_SLC Register]] for one or both meetings.<br />
<br />
== Agenda Items ==<br />
At the moment this is a free-form list of items suggested for discussion.<br />
<br />
# Have Tanya give a presentation on implementation of 'regulates' and the work that she and David and Chris (and others) have done in this area. 'Regulates' will go live at the end of March, so there may be discussion points on this. We will also discuss 'regulation of biological quality' and how their negative and positive children relate.<br />
# Discuss how we are going to handle function terms such as activators and inhibitors. When do we create them and how do they relate to processes and other functions. (David and Tanya)<br />
# Discuss how we are going to handle 'response to drug' SF 1242405 terms. Are they normal biological processes? (David and Tanya)<br />
# Discuss function-process links. What relationships should we use? Who will make the assertions?(Harold, Jen & Chris)<br />
## See current work and discussions [[http://gocwiki.geneontology.org/index.php/Function-Process_Links |Here]]<br />
# (sigh) evidence codes<br />
# (from ref genomes group): Would it be useful to add the 'comprehensively annotated' tag to all genes (not just the ref genome genes)? Either in the gene association file or in the database somehow<br />
# At one of our meetings Chris suggested we might keep an archive of gene sets used in publications that were analyzed using GO. Should we do this? (David)<br />
# Collaboration with other projects<br />
## PRO: Protein Ontology (Harold)<br />
## Reactome<br />
## Panther<br />
## NCBO<br />
## MP-PATO<br />
## KARO<br />
# Annotation Objects: how to handle GO annotation to specific isoforms, modified proteins, etc. (Harold)<br />
# Report results of experiment on finding annotation errors using GO-taxon links. (Jen)</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12092Signaling ontology structure documentation2008-03-26T14:35:01Z<p>Jclark: </p>
<hr />
<div>==Top categories==<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_ontology_structure_documentation&diff=12091Signaling ontology structure documentation2008-03-26T14:34:31Z<p>Jclark: New page: ==Top categories== [i]signaling systems grouped by chemical properties of the signal ---[i]hydrophobic molecule-mediated signaling ---[i]hydrophilic molecule-mediated signaling ...</p>
<hr />
<div>==Top categories==<br />
<br />
<br />
[i]signaling systems grouped by chemical properties of the signal <br />
---[i]hydrophobic molecule-mediated signaling <br />
---[i]hydrophilic molecule-mediated signaling <br />
<br />
[i]signaling systems grouped by outcome of the signal<br />
<br />
<br />
<br />
==Sub-groups==<br />
<br />
[i]hydrophobic molecule-mediated signaling <br />
---[i]nitrous oxide-mediated signaling<br />
---[i]carbon monoxide-mediated signaling<br />
<br />
[i]hydrophilic molecule-mediated signaling <br />
<br />
<br />
[i]signaling to control gene expression<br />
---[i]primary response<br />
---[i]secondary response</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling&diff=12090Signaling2008-03-26T14:27:45Z<p>Jclark: </p>
<hr />
<div>Placeholder - Work on signal transduction, signaling pathways, etc. will be documented here.<br />
<br />
Mailing list:<br />
<br />
Pascale Gaudet<br><br />
Petra Fey<br><br />
Jennifer Deegan<br><br />
David Hill<br><br />
Alex Diehl?<br><br />
<br />
<br />
[[Signaling sourceforge items]]<br />
<br />
[[Signaling - pointers from the community]]<br />
<br />
[[Signaling text book summary]]<br />
<br />
[[Signaling ontology structure documentation]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12087Signaling text book summary2008-03-26T14:26:52Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
==Some Intracellular signaling proteins behave like molecular switches==<br />
<br />
2 classes:<br />
<br />
Both use gain or loss of a phosphate group to determine if a protein is active or inactive. <br />
<br />
===Proteins activated or inactivated by phosphorylation===<br />
<br />
p845<br />
<br />
<br />
protein kinase ----------><br />
(adds phosphate group)<br />
<br />
<-------------protein phosphatase<br />
(remove phosphate groups)<br />
<br />
<br />
===GTP-binding proteins===<br />
<br />
active state when GTP is bound<br />
inactive state when GDP is bound. <br />
<br />
Once activated, these proteins have intrinsic GTPase activity and shut themselves off by hydrolysing their bound GTP to GDP. <br />
<br />
Two types of GTP-binding proteins:<br />
<br />
'''A) Large trimeric GTP-binding proteins (G proteins)'''<br />
<br />
*These relay the signals from G protein-linked receptors.<br />
<br />
'''B) Monomeric GTPases'''<br />
<br />
*also help relay intracellular signals<br />
*also involved in regulating vesicular traffic + other processes in eukaryotic cells. <br />
<br />
==Scaffold proteins==<br />
<br />
Allow different response to the same signals in different cells, by organizing groups of interacting signaling proteins into signaling complexes. p846.<br />
<br />
==Gradients in signal concentration==<br />
<br />
p849 explains ways in which the response to a signal can be work with the gradient of the signal molecule concentration. <br />
<br />
==Effects that persist after the signal has gone==<br />
<br />
P850 shows why some signals have a permenant effect even after the signal has gone. This is seen in the permeneant change of cell idenetity that persist after the singal has disappeared. <br />
<br />
==Sensitivity adjustment==<br />
<br />
p851 shows how cells can adjust their sensitivity to signals. Includes '''adaptation''' and '''desensitization'''.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).<br />
<br />
==Ontology thoughts==<br />
<br />
We could divide signal molecule types based on whether they are hydrophilic (not able to cross membrane) or hydrophobic (able to penetrate membrane).<br />
<br />
==Notes==<br />
<br />
I have read the chapter up to p852, where these is a much more detailed section on some of the types. <br />
<br />
I have not yet read the plant section at the end.</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12080Signaling text book summary2008-03-26T13:25:29Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
==Some Intracellular signaling proteins behave like molecular switches==<br />
<br />
2 classes:<br />
<br />
Both use gain or loss of a phosphate group to determine if a protein is active or inactive. <br />
<br />
===Proteins activated or inactivated by phosphorylation===<br />
<br />
p845<br />
<br />
<br />
protein kinase ----------><br />
(adds phosphate group)<br />
<br />
<-------------protein phosphatase<br />
(remove phosphate groups)<br />
<br />
<br />
===GTP-binding proteins===<br />
<br />
active state when GTP is bound<br />
inactive state when GDP is bound. <br />
<br />
Once activated, these proteins have intrinsic GTPase activity and shut themselves off by hydrolysing their bound GTP to GDP. <br />
<br />
Two types of GTP-binding proteins:<br />
<br />
'''A) Large trimeric GTP-binding proteins (G proteins)'''<br />
<br />
*These relay the signals from G protein-linked receptors.<br />
<br />
'''B) Monomeric GTPases'''<br />
<br />
*also help relay intracellular signals<br />
*also involved in regulating vesicular traffic + other processes in eukaryotic cells. <br />
<br />
==Scaffold proteins==<br />
<br />
Allow different response to the same signals in different cells, by organizing groups of interacting signaling proteins into signaling complexes. p846.<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12079Signaling text book summary2008-03-26T13:23:26Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
==Some Intracellular signaling proteins behave like molecular switches==<br />
<br />
2 classes:<br />
<br />
Both use gain or loss of a phosphate group to determine if a protein is active or inactive. <br />
<br />
===Proteins activated or inactivated by phosphorylation===<br />
<br />
p845<br />
<br />
<br />
protein kinase ----------><br />
(adds phosphate group)<br />
<br />
<-------------protein phosphatase<br />
(remove phosphate groups)<br />
<br />
<br />
===GTP-binding proteins===<br />
<br />
active state when GTP is bound<br />
inactive state when GDP is bound. <br />
<br />
Once activated, these proteins have intrinsic GTPase activity and shut themselves off by hydrolysing their bound GTP to GDP. <br />
<br />
Two types of GTP-binding proteins:<br />
<br />
'''A) Large trimeric GTP-binding proteins (G proteins)'''<br />
<br />
*These relay the signals from G protein-linked receptors.<br />
<br />
'''B) Monomeric GTPases'''<br />
<br />
*also help relay intracellular signals<br />
*also involved in regulating vesicular traffic + other processes in eukaryotic cells. <br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12078Signaling text book summary2008-03-26T13:19:17Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
==Some Intracellular signaling proteins behave like molecular switches==<br />
<br />
2 classes:<br />
<br />
Both use gain or loss of a phosphate group to determine if a protein is active or inactive. <br />
<br />
===Proteins activated or inactivated by phosphorylation===<br />
<br />
p845<br />
<br />
<br />
protein kinase ----------><br />
(adds phosphate group)<br />
<br />
<-------------protein phosphatase<br />
(remove phosphate groups)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12077Signaling text book summary2008-03-26T13:19:03Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
==Some Intracellular signaling proteins behave like molecular switches==<br />
<br />
2 classes:<br />
<br />
Both use gain or loss of a phosphate group to determine if a protein is active or inactive. <br />
<br />
===Proteins activated or inactivated by phosphorylation===<br />
<br />
p845<br />
<br />
<br />
protein kinase ----------><br />
(adds phosphate group)<br />
<br />
<-------------protein phosphatase<br />
(remove phosphate groups)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12076Signaling text book summary2008-03-26T13:18:42Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
==Some Intracellular signaling proteins behave like molecular switches==<br />
<br />
2 classes:<br />
<br />
Both use gain or loss of a phosphate group to determine if a protein is active or inactive. <br />
<br />
===Proteins activated or inactivated by phosphorylation===<br />
<br />
p845<br />
<br />
<br />
protein kinase ----------><br />
(adds phosphate group)<br />
<br />
<-------------protein phosphatase<br />
(remove phosphate groups)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12075Signaling text book summary2008-03-26T13:18:20Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
==Some Intracellular signaling proteins behave like molecular switches==<br />
<br />
2 classes:<br />
<br />
Both use gain or loss of a phosphate group to determine if a protein is active or inactive. <br />
<br />
===Proteins activated or inactivated by phosphorylation===<br />
<br />
p845<br />
<br />
<br />
protein kinase ----------><br />
(adds phosphate group)<br />
<br />
<-------------protein phosphatase<br />
(remove phosphate groups)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12068Signaling text book summary2008-03-25T16:24:19Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permanent due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Thaw_Mail&diff=12067Thaw Mail2008-03-25T16:04:08Z<p>Jclark: </p>
<hr />
<div>==Thaw Mail==<br />
<br />
<br />
Hi,<br />
<br />
The 'regulates' relationships, the electron transport changes, and the new cvs layout have been implemented, and the ontology editing freeze is now over. <br />
For those who edit the ontologies, please now *only* edit the ontology file go/ontology/editors/gene_ontology_write.obo <br />
as your changes will otherwise be automatically over-written. If you are having trouble seeing the 'regulates' links in OBO-Edit, make sure<br />
that your Global Filters are updated to remove this one: "Select links where Type that have a 'Is Transitive'" (and you could also try restarting).<br />
<br />
The layout of the go/ontology directory has been overhauled for a couple of reasons:<br />
<br />
1) To simplify file identification for users.<br />
2) To provide a private version of the ontology file, in <br />
which we can test for file problems before we release a <br />
separate public copy for users. We are hoping that this will <br />
help reduce the incidence of small file errors causing big<br />
problems for daily database loads at the mods. The new file <br />
will also enable us to add features to the private file for <br />
testing, but to have them stripped out in the public version.<br />
This helps us get new features fully tested within the file, <br />
rather than having a rushed merge and release.<br />
<br />
The old cvs structure will continue to be supported:<br />
<br />
go/<br />
ontology/<br />
gene_ontology.obo (OBO 1.0 format)<br />
gene_ontology_edit.obo (OBO 1.2 format)<br />
<br />
<br />
The new structure looks like this:<br />
<br />
go/<br />
ontology/<br />
obo_format_1_0/<br />
gene_ontology.1_0.obo (OBO 1.0 format)<br />
obo_format_1_2/<br />
gene_ontology.1_2.obo (OBO 1.2 format)<br />
editors/<br />
gene_ontology_write.obo (OBO 1.2 format)<br />
<br />
<br />
Ontology editors should only edit gene_ontology_write.obo.<br />
Users who wish to download a copy of the file in OBO 1.0 format should use gene_ontology.1_0.obo.<br />
Users who wish to download a copy of the file in OBO 1.2 format should use gene_ontology.1_2.obo.<br />
<br />
Please note that the script is not yet in place to handle the file conversions between <br />
the write file and the 1.0 and 1.2 files, but we will receive a mail from SGD via the GO list when it is. <br />
<br />
Thanks for reading. :-)<br />
<br />
Jen<br />
<br />
<br />
Further details here:<br><br />
http://wiki.geneontology.org/index.php/Ontology_CVS_Directory_Layout_Overhaul#Proposed_new_layout</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12066Signaling text book summary2008-03-25T15:55:17Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
==Large intracellular signaling proteins==<br />
<br />
several types:<br />
<br />
===1. Relay proteins===<br />
<br />
These simply pass the message to the next signaling component in the chain.<br />
<br />
===2. Messenger proteins=== <br />
<br />
These carry the signal from one part of the cell to another, such as from the cytosol to the nucleus.<br />
<br />
===3. Adaptor proteins===<br />
<br />
These link one signaling protein to another, without themselves conveying a signal.<br />
<br />
===4. Amplifier proteins===<br />
These are usually either enzymes or ion channels, greatly increase the signal they receive, either by producing large amounts of small intracellular mediators or by activating large numbers of downstream intracellular signaling proteins. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade.<br />
<br />
===5. Transducer proteins===<br />
These convert the signal into a different form. The enzyme that makes cyclic AMP is an example: it both converts the signal and amplifies it, thus acting as both a transducer and an amplifier.<br />
<br />
===6. Bifurcation proteins===<br />
These spread the signal from one signaling pathway to another.<br />
<br />
===7. Integrator proteins===<br />
These receive signals from two or more signaling pathways and integrate them before relaying a signal onward.<br />
<br />
===8. Latent gene regulatory proteins===<br />
These are activated at the cell surface by activated receptors and then migrate to the nucleus to stimulate gene transcription. <br />
<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permenant due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12065Signaling text book summary2008-03-25T15:49:55Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
==First Messengers==<br />
<br />
These are extracellular signals p843<br />
<br />
==Second messengers==<br />
<br />
*These are small intercellular signaling molecules<br />
* They diffuse to membrane or cytosol depending on solubility. <br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permenant due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12064Signaling text book summary2008-03-25T15:48:11Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surface receptor proteins==<br />
<br />
3 kinds:<br />
<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surface receptor proteins===<br />
<br />
*Mostly to do with the protein kinases. <br />
*Ligand-binding enables phosphorylation of specific proteins in target cell. <br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different signals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are permenant due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12063Signaling text book summary2008-03-25T15:46:42Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surfacce receptor proteins==<br />
<br />
3 kinds:<br />
<br />
<br />
===1) Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===2) G-Protein linked cell surface receptor proteins===<br />
<br />
===3) Enzyme linked cell surfacce receptor proteins===<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different singals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are premenant due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Signaling_text_book_summary&diff=12062Signaling text book summary2008-03-25T15:46:10Z<p>Jclark: </p>
<hr />
<div>From Molecular Biology of the Cell - Cell Communication Chapter<br />
<br />
<br />
==Contact-dependent signaling ==<br />
<br />
development and immune system<br />
p833<br />
<br />
==local mediators (paracrine signaling) ==<br />
p834<br />
<br />
*signals don't travel far<br />
*soon taken up<br />
*rapidly destroyed<br />
*immobilised<br />
<br />
==long distance signals - nervous system==<br />
<br />
p834<br />
<br />
* nerve cell - electric impulses (action potentials) fast (up to 100m/s)<br />
*neurotransmitters<br />
*chemical synapses<br />
<br />
see chapter 11 for synaptic signaling processes.<br />
<br />
==Long distance signals - hormones for endocrine cells==<br />
<br />
*transported via the bloodstream<br />
* slow acting<br />
low concentration -> large effects. <br />
<br />
<br />
==Autocrine signaling==<br />
* Cell secretes a signal that can bind back to its own receptors or those of the same cell type.<br />
* For example in development this is used to maintain cell identity after initial differentiation.<br />
* Also used to make sure all adjacent cells differentiate in the same way. <br />
<br />
==Gap junctions==<br />
* Allows cell to communicate with each other by having a tunnel across the plasma membrane<br />
* Dye can squirt through the tunnels and this is how people spot them experimentally. <br />
* Patterns of making and breaking gap junctions are important in development.<br />
<br />
==Nitrous Oxide==<br />
<br />
*NO and CO and other similar small hydrophobic molecules are able to pass straight through the membrane and are used as signals. <br />
*These bind to intracellular receptor proteins. <br />
*e.g. steroid hormones, thyroid hormones, retinoids, vitamin D. <br />
*The signal molecules bind to the receptor molecules, which then become activated, and are able to bind to DNA to regulate transcription. <br />
*The receptors are all members of the nuclear receptor super family.<br />
*This leads to the primary and secondary response:<br />
<br />
<br />
<br />
===Signaling to control gene expression - Primary response===<br />
<br />
* ligands bound by hormones bing to gene regulatory bits and turn on expression.<br />
* This takes about 30 minutes<br />
<br />
===Signaling to control gene expression - Secondary response===<br />
<br />
* Protein products made in the primary response activate other genes to produce a delayed secondary response. <br />
<br />
N.B. This means that a simple hormonal trigger can produce a very complex pattern of gene expression.<br />
<br />
==Cell surfacce receptor proteins==<br />
<br />
3 kinds:<br />
<br />
<br />
===Ion-channel linked cell surfacce receptor proteins===<br />
<br />
N.B. these are the transmitter-gated ion channels that were updated in the transport overhaul. The top level term is already in place. <br />
p842<br />
<br />
===G-Protein linked cell surface receptor proteins===<br />
<br />
===Enzyme linked cell surfacce receptor proteins===<br />
<br />
<br />
<br />
==Some general features in signaling==<br />
<br />
*Cells are bathed in hundreds of different singals all the time. <br />
* response of different cells to the same signal can be depend on the internal machinery, even if the receptor is the same. <br />
* some effects on cell are premenant due to cell memory - though this is usually not the case. (chap 7 + 21) <br />
* half life is important as signal concentration cannot change quickly if the signal is not broken down quickly. <br />
* e.g. if phosphorylation is an important part of signaling then there must also be rapid dephosphorylation to keep background signal level low.<br />
* speed of response of a cell also depends on turnover of internal chemical (p837-838).</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Thaw_Mail&diff=12061Thaw Mail2008-03-25T15:42:40Z<p>Jclark: </p>
<hr />
<div>==Thaw Mail==<br />
<br />
<br />
Hi,<br />
<br />
The 'regulates' relationships, the electron transport changes, and the new cvs layout have been implemented, and the ontology editing freeze is now over. <br />
For those who edit the ontologies, please now *only* edit the ontology file go/ontology/editors/gene_ontology_write.obo <br />
as your changes will otherwise be automatically over-written. If you are having trouble seeing the 'regulates' links in OBO-Edit, make sure<br />
that your Global Filters are updated to remove this one: "Select links where Type that have a 'Is Transitive'" (and you could also try restarting).<br />
<br />
The layout of the go/ontology directory has been overhauled for a couple of reasons:<br />
<br />
1) To simplify file identification for users.<br />
2) To provide a private version of the ontology file, in <br />
which we can test for file problems before we release a <br />
separate public copy for users. We are hoping that this will <br />
help reduce the incidence of small file errors causing big<br />
problems for daily database loads at the mods. The new file <br />
will also enable us to add features to the private file for <br />
testing, but to have them stripped out in the public version.<br />
This helps us get new features fully tested within the file, <br />
rather than having a rushed merge and release.<br />
<br />
The old cvs structure will continue to be supported:<br />
<br />
go/<br />
ontology/<br />
gene_ontology.obo (OBO 1.0 format)<br />
gene_ontology_edit.obo (OBO 1.2 format)<br />
<br />
<br />
The new structure looks like this:<br />
<br />
go/<br />
ontology/<br />
obo_format_1_0/<br />
gene_ontology.1_0.obo (OBO 1.0 format)<br />
obo_format_1_2/<br />
gene_ontology.1_2.obo (OBO 1.2 format)<br />
editors/<br />
gene_ontology_write.obo (OBO 1.2 format)<br />
<br />
<br />
Ontology editors should only edit gene_ontology_write.obo.<br />
Users who wish to download a copy of the file in OBO 1.0 format should use gene_ontology.1_0.obo.<br />
Users who wish to download a copy of the file in OBO 1.2 format should use gene_ontology.1_2.obo.<br />
<br />
The script is not yet in place to handle the file conversions between the write file and the 1.0 and 1.2 files but we will have a mail from SGD to the go list when it is. <br />
<br />
Thanks for reading. :-)<br />
<br />
Jen<br />
<br />
<br />
Further details here:<br><br />
http://wiki.geneontology.org/index.php/Ontology_CVS_Directory_Layout_Overhaul#Proposed_new_layout</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Ontology_CVS_Directory_Layout_Overhaul_2007_(Archived)&diff=12060Ontology CVS Directory Layout Overhaul 2007 (Archived)2008-03-25T15:42:04Z<p>Jclark: </p>
<hr />
<div>== Rationale ==<br />
<br />
The current layout is confusing, with the edit file serving two purposes: an editors version and an obof1.2 version<br />
<br />
Purpose: provide buffer between ontology users and editors to allow implementation of new features in a way that is non-disruptive<br />
<br />
Currently we have<br />
<br />
go/<br />
ontology/<br />
gene_ontology.obo<br />
gene_ontology_edit.obo<br />
<br />
this was designed to be a separate editors and for-public version of the ontology. However, the editors version has been advertised as the file to download for the public wishing to get obof1.2 features.<br />
<br />
== Timeline ==<br />
<br />
=== Immediate timeline ===<br />
<br />
The new layout will be phased in from March 18-25 2007.<br />
<br />
This will be tied in with the introduction of the regulates relation<br />
<br />
# Midnight Pacific time March 18 (8 am, 3/19 Jen's time) : Begin freeze.<br />
#* Jen merges electron transport changes into gene_ontology_edit.obo, then let's Chris know that he can start file conversion<br />
#* This marks the last ever manual edit to gene_ontology_edit.obo<br />
# March 19: Add regulates relations - keep in scratch/ then cp to gene_ontology_write<br />
# March 20: Switch edit files: gene_ontology_write.obo open for business.<br />
#* Editors (David, Tanya, Jen only) can edit new file for QC purposes only. However, new changes remain largely invisible to general public<br />
# March 20-25: Switch script to use gene_ontology_write as source. See software TODO below<br />
# Freeze period will last until March 25th, x am Pacific when Chris puts up gene_ontology_write.obo as editor's file. Chris will email go list to say that new file is available for editing. <br />
# March 26+: Announce changes to community<br />
<br />
=== Future changes ===<br />
<br />
Dates to be determined<br />
<br />
# Extract slims from for-public version<br />
#* (retain in go_write for ease of maintenance)<br />
# Introduce stanza timestamps to write version<br />
# Add a obof1.3 export directory<br />
<br />
== Proposed new layout ==<br />
<br />
The layout here is for the cvs tree. This is also reflected in the public URLs for GO.<br />
E.g the following are equivalent:<br />
<br />
* go/ontology/gene_ontology_edit.obo (CVS)<br />
* http://www.geneontology.org/ontology/gene_ontology_edit.obo (WWW)<br />
<br />
This is the proposed structure:<br />
<br />
go/<br />
ontology/<br />
<br />
gene_ontology.obo <br />
-- The current for-public version of GO.<br />
-- Format: obof1.0 (currently)<br />
-- We reserve the right to switch to obof1.2, and any future versions,<br />
-- given sufficient lead time for file consumers to change software.<br />
-- If you wish to use a file that is *guaranteed* to be obof1.0, please consider<br />
-- go/ontology/obo_format_1_0/gene_ontology.1_0.obo<br />
<br />
gene_ontology_edit.obo <br />
-- ** DEPRECATED [March 25 2008] **<br />
-- Format: obof1.2<br />
-- Use of this file is no longer recommended after March 25 2008<br />
-- Please use go/ontology/obo_format_1_2/gene_ontology.1_2.obo instead<br />
-- (the contents should be identical)<br />
-- This file path will be fully supported throughout 2008 and possibly indefinitely<br />
<br />
obo_format_1_0/<br />
<br />
README<br />
-- contains links to obof1.0 documentation<br />
<br />
gene_ontology.1_0.obo<br />
-- Format: obof1.0<br />
-- Recommended instead of: go/ontology/gene_ontology.obo<br />
<br />
obo_format_1_2/<br />
<br />
README<br />
-- contains links to obof1.2 documentation<br />
<br />
gene_ontology.1_2.obo <br />
-- Format: obof1.2<br />
-- Must be used instead of: go/ontology/gene_ontology.obo<br />
<br />
editors/<br />
<br />
README<br />
<br />
gene_ontology_write.obo<br />
-- You should only use this file path if you are editing the live ontology.<br />
-- We do not recommend use of this file for non-editors. The file may<br />
-- contain experimental new features or tags that are filtered out in<br />
-- the for-public version.<br />
-- Caveat emptor!<br />
<br />
There is further explanation here:<br><br />
http://wiki.geneontology.org/index.php/Thaw_Mail<br />
<br />
<br />
== Software/Admin TODO ==<br />
<br />
Fix scripts for updating .obo files and .go files.<br />
<br />
The sequence of events is as follows:<br />
<br />
# generate obo_format_1_2/gene_ontology.1_2.obo<br />
#* at first this will be a direct cp of editors/gene_ontology_write.obo<br />
#* in the future it may use obo2obo (for example, to separate out slims)<br />
# generate obo_format_1_0/gene_ontology.1_0.obo<br />
#* using obo2obo<br />
# generate deprecated files<br />
#* using cp<br />
# cvs commit<br />
<br />
== FAQ ==<br />
<br />
=== will this break scripts / configurations or lead to dead or stale links? ===<br />
<br />
No, absolutely not. The change will be invisible to most uses as <br />
http://www.geneontology.org/ontology/gene_ontology_edit.obo and<br />
http://www.geneontology.org/ontology/gene_ontology.obo will continue to be contain up-to-date (< 24hrs) versions of the ontologies in .obo format.<br />
<br />
We may *eventually* deprecate http://www.geneontology.org/ontology/gene_ontology_edit.obo - however, we would not have stale URLs. We could do a URL redirect (http code 304) to http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo<br />
<br />
=== when should I change my scripts / configuration? ===<br />
<br />
Any time after March 25 2008. There is no set window in which this needs to be done. http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo will be synonymous with http://www.geneontology.org/ontology/gene_ontology_edit.obo<br />
<br />
== See Also ==<br />
<br />
[[Versioning_Proposal]]</div>Jclarkhttps://wiki.geneontology.org/index.php?title=Thaw_Mail&diff=12058Thaw Mail2008-03-25T15:37:12Z<p>Jclark: </p>
<hr />
<div>==Thaw Mail==<br />
<br />
<br />
Hi,<br />
<br />
The 'regulates' relationships, the electron transport changes, and the new cvs layout have been implemented, and the ontology editing freeze is now over. <br />
For those who edit the ontologies, please now *only* edit the ontology file go/ontology/editors/gene_ontology_write.obo <br />
as your changes will otherwise be automatically over-written. If you are having trouble seeing the 'regulates' links in OBO-Edit, make sure<br />
that your Global Filters are updated to remove this one: "Select links where Type that have a 'Is Transitive'" (and you could also try restarting).<br />
<br />
The layout of the go/ontology directory has been overhauled for a couple of reasons:<br />
<br />
1) To simplify file identification for users.<br />
2) To provide a private version of the ontology file, in <br />
which we can test for file problems before we release a <br />
separate public copy for users. We are hoping that this will <br />
help reduce the incidence of small file errors causing big<br />
problems for daily database loads at the mods. The new file <br />
will also enable us to add features to the private file for <br />
testing, but to have them stripped out in the public version.<br />
This helps us get new features fully tested within the file, <br />
rather than having a rushed merge and release.<br />
<br />
The old cvs structure will continue to be supported:<br />
<br />
go/<br />
ontology/<br />
gene_ontology.obo (OBO 1.0 format)<br />
gene_ontology_edit.obo (OBO 1.2 format)<br />
<br />
<br />
The new structure looks like this:<br />
<br />
go/<br />
ontology/<br />
obo_format_1_0/<br />
gene_ontology.1_0.obo (OBO 1.0 format)<br />
obo_format_1_2/<br />
gene_ontology.1_2.obo (OBO 1.2 format)<br />
editors/<br />
gene_ontology_write.obo (OBO 1.2 format)<br />
<br />
<br />
Ontology editors should only edit gene_ontology_write.obo.<br />
Users who wish to download a copy of the file in OBO 1.0 format should use gene_ontology.1_0.obo.<br />
Users who wish to download a copy of the file in OBO 1.2 format should use gene_ontology.1_2.obo.<br />
<br />
The script is not yet in place to handle the file conversions between the write file and the 1.0 and 1.2 files but we will have a mail from SGD to the go list when it is. <br />
<br />
Thanks for reading. :-)<br />
<br />
Jen</div>Jclark