https://wiki.geneontology.org/api.php?action=feedcontributions&user=Vpetri&feedformat=atomGO Wiki - User contributions [en]2024-03-29T13:54:37ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Gohelp_rota&diff=58393Gohelp rota2015-09-09T14:19:44Z<p>Vpetri: </p>
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<div>[[Category:Advocacy and Outreach]]<br />
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This is the rotation schedule for the GO HelpDesk.<br />
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{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Week beginning on<br />
|-<br />
| '''Petra'''<br />
| August 17th<br />
|-<br />
| '''Tanya'''<br />
| August 24th (swapped with Paola)<br />
|-<br />
| '''Maria'''<br />
| August 31st<br />
|-<br />
| '''Moni'''<br />
| September 7th<br />
|-<br />
| '''Victoria'''<br />
| September 14th (swapped with Rachel)<br />
|-<br />
| '''Kimberly'''<br />
| September 21st<br />
|-<br />
| '''David OS'''<br />
| September 28th<br />
|-<br />
| '''Rachael'''<br />
| October 5th (Victoria takes this week)<br />
|-<br />
| '''Harold'''<br />
| October 12th<br />
|-<br />
| '''Edith'''<br />
| October 19th<br />
|-<br />
| '''Donghui'''<br />
| October 26th<br />
|-<br />
| '''Rama'''<br />
| November 2nd<br />
|-<br />
| '''Tanya'''<br />
| November 9th<br />
|-<br />
| '''Paola'''<br />
| November 16th<br />
|-<br />
| '''Melanie'''<br />
| November 23rd<br />
|-<br />
| '''Kimberly'''<br />
| November 30th<br />
|-<br />
| '''Moni'''<br />
| December 7th<br />
|-<br />
| '''Harold'''<br />
| December 14th<br />
|-<br />
|-|-)<br />
|}<br />
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'''Notes:'''<br />
* Victoria, Petra, Helen (Attrill), Rachael, and Becky have offered to be on the rotation twice a year.<br />
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:* [[JIRA issues|GO-Help JIRA issues]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Binding_Terms_Survey_Comments&diff=20291Binding Terms Survey Comments2009-06-08T13:56:02Z<p>Vpetri: </p>
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<div>Back to binding terms conference call [http://wiki.geneontology.org/index.php/Binding_Terms_Conference_Call_Information wiki]<br />
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Please note that these comments are added manually and therefore if additional modifications are made to the comments field of the survey please email r.lovering@ucl.ac.uk providing something from the text of the question before modification and the text after so that the new comment can be added below.<br />
== Question 1 ==<br />
'''The GO consortium should remove all annotations which describe catalytic domain substrate binding, associated with catalytic activities or transport proteins, and no longer annotate these interactions.'''<br />
<br />
Comments:<br />
<br />
#Terms should be annotated to binding terms only if there was an experiment that demonstrated binding. There should not be coannotation for substrate binding if an experiment demonstrates catalytic activity. Instead the catalytic annotation should be made. <br />
#I disagree, but one should only annotate to binding if binding is directly demonstrated. <br />
#I dissagree with the proposal. If paper has experiment for a kinase that demonstrates ATP binding, then we should annotate it. There must be an experiment since the annotation would be an IDA. What if an unknown protein is shown to bind DNA; then 5 years later, it is shown to have helicase activity. It would be counterproductive to then have to remove the first annotation.<br />
#Sympathetic to the proposal but still not completely decided. On the wiki page the question was asked: "Are there cases where a user would want to search for gene products that bind a particular substrate but have different molecular functions? " One answer to this springs to mind, the ubiquitin conugating E2 enzymes. Many of these proteins have lost the catalytic function yet nevertheless bind ubiquitin. For instance, hMMS2/UBE2V2 (catalytically inactive) forms a heterodimer with UBC13 (catalytically active). hMMS2/UBE2V2 binds the donor ubiqutin and orients the ubiquitin lys-63 toward the acceptor site in UBC13. In this case we would have to annotate one member of the heterodimer as ubiquitin-binding and the other one as not doing so, as this subunit is also catalytically active. While I think you can justify this, many users would probably find this confusing. Another example are the argonaute proteins, EIF2C1/AGO1 EIF2C2/AGO2, EIF2C3/AGO3 and EIF2C4/AGO4. All 4 of these proteins bind to an siRNA or miRNA, which serves as a guide for complementary mRNAs. In the case of AGO1, 3 and 4, the bound complementary mRNA is subject to translational repression. Therefore for these 3 proteins you would annotate to mRNA binding as the mRNA is not really a substrate and they lack any kind of catalytic activity. AGO2 on the other hand does have a catalytic activity but also acts like AGO1/3/4. For AGO2 the mRNA is either subject to translational repression (when the miRNA exhibits imperfect complementarity), or subject to endonucleolytic cleavage by AGO2 (generally when the complementarity is perfect - see GO:0070551). So AGO2 could be annotated to mRNA binding but only for papers that demonstrated translational repression, not cleavage. Again I think users would probably find this confusing.<br />
#I agree that if there is evidence supporting a catalytic activity then related binding annotations are not useful. However, there are many cases where for example a suspected GTPase has been demonstrated to bind GTP, but has not been shown to catalyze the hydrolysis, in which case it becomes GTP binding or nothing. So I would say my vote is a qualified yes, its a good idea but what would we do in cases like this? <br />
#I like Jim's suggestion of retaining high level binding terms. Realistically, we are not going to have time to revaluate every binding annotation so by moving things to a generic binding term as least we don't lose the functional info and the retrofit is feasible. However, given that we are not set up for col 16 due to database constraints and also our curators are likely resist the additional burden of having to figure out the appropriate chebi IDs, I suspect there will be a loss of info in terms of what the interacting molecules are for new annotations.<br />
#This is entire survey too binary - in principle, I agree we need to limit the scope of the "binding" terms but keep in mind that there are biological functional "binding" functions.<br />
#If i have evidence for GTPase activity, I would annotate it to just that term. Dual annotation doesn't make sense. But if I have evidence, say based on some domain comparison, that the gp has ATP binding domain, then I would annotate to just ATP binding with ISS.<br />
#Annotate at the level of what function is shown in the experiment. If the experiment shows GTPase activity, then annotate to GTPase activity. If it shows GTP binding, then annotate to GTP binding.<br />
# It happens that the example is a GTPase and GTP binding looks pretty obvious, it's not always the case but it shouldn't matter. If the authors have measured both, then both should be reported.<br />
<br />
== Question 2 ==<br />
'''Change the definition of 'x binding' terms to explicitly exclude catalytic domain substrate binding.<br />
'''<br />
Comments:<br />
#For all the questions involving x binding redefinition, I am opposed to precomposed terms of the type "x binding"<br />
#Do not change the definition, change annotation practice.<br />
#When I read a paper and they show that it binds GTP, then I would like to be able to curate that fact, especially when I have no other molecular function information to give. The author is unlikely to make any unequivocal statement stating that it binds GTP but definitely doesn't hydrolyze it. And, if I have to go read other papers that do separate experiments which show that it is "NOT" hydrolyzed, can I really use the original reference as my sole source for that annotation? It seems that I have to draw an inference from multiple experiments to know that it does A (binds GTP), but definitely doesn't do B (use it as a substrate). I like to try to limit my annotations to what is directly shown by a particular experiment when possible.<br />
#Again, binding should only be annotated if it is directly demonstrated.<br />
#It would be an ENORMOUS amount of work to go back through annotations to decide whether the term was used 'correctly' or not<br />
#I am not sure removing all of the "incorrect" annotations is necessary. I view it as "redundant information", which should be eliminated because it doesn't add information. <br />
#Annotation of such binding should only be made when the experiment specifically shows such binding, when the point of the experiment is to prove such binding, not inferred by the annotator because of the presence or requirement of a cofactor or reagent in the reaction mix. <br />
#In many older biochemistry papers, binding was used as an indicator that the protein might have catalytic activity on the binding partner. Ex: one step in the purification of a helicase might be a DNA column, but other proteins that bind to the column might not have helicase activity. It would still be useful to capture the DNA binding activity of these proteins even if they are subsequently shown to have catalytic activity on DNA. Also, it's useful to have a sense of history in GO, i.e. what was known when, so that we can see how partial information (DNA binding) might develop into a clearer picture (topoisimerase).<br />
#I agree with all of the cons; I reject all of the pros.<br />
#I don't see why this applies: "In future curators would not be able to annotate proteins for which the only information presented is that they bind 'x' (with no indication of the context of this binding - is it a substrate/cofactor/something else?). " If they bind 'x' then they could be annotated as such. In the future if 'x' is discovered to be a substrate, the previous annotation would have to be removed. <br />
#I dont think it's possible to do annotation if one annotation (x binding) depends on another annotation (here, catalytic activity).<br />
#This seems to me to be more in line with the intentions of GO and I am not sure that losing these types of annotation is really a bad thing in most cases. However there are perhaps specific cases where this could be very confusing for users as described comments on point 1. On the other hand, if the only information available for a protein is that it binds zinc, or a lipid etc, then that is not much information at all and the significance of a paper that publishes only these kinds of results is perhaps questionable. If you have 2 papers and paper 1 shows cholesterol binding and paper 2 demonstrates a role for the protein as a cholesterol transport protein, I would annotate paper 2 and leave paper 1 aside. See also point 3 below.<br />
#On the condition that there were terms for non-substrates (ie cofactors, allosteric regulators, etc). <br />
#See above. Same concerns if this is all that has been experimentally determined.<br />
#I don't think this will work. While we all know that we should read definitions before annotating if you leave the terms in without making this change explicit in the name curators will keep using them incorrectly. Also, what do you do if it isn't clear whether it is a substrate or not? If you don't annotate you lose the 'binding function' info - if you do annotate it may turn out later to be wrong. GO annotation is only one aspect of the data that is captured from a paper - curators simply don't have time to revise old data in the light of new info during routine curation. Once an annotation is made it is likely to stay there for a long time.<br />
#It is often not possible to make the distinction, e.g. because there is insufficient information. It would be paradoxical to annotate "GTP-binding" only when GTP has a regulatory rule. Plus, would be very difficult to implement.<br />
#Given your definition, it doesn't seem like the con "curators would not be able to annotate proteins with limited information" is a valid point, as it would only apply to proteins that contain catalytic domains (which wouldn't fall into the "all we know is that it binds protein" category).<br />
#I don't think i understand the con part! If the only evidence you have is that gpX has a ATP binding domain, then that is all the annotation you can make. gp can bind to ATP for so many reasons, not always for hydrolysis?<br />
#I think that if curators annotate a catalytic substrate to binding that is OK, but I think the practice should be discouraged. I want to slow down the proliferation of binding terms for every possible substrate in the biological realm.<br />
#What if 'catalytic domain substrate' binding is what the assay demonstrates? We'd want to capture that.<br />
#Many times the Km, an important parameter, is determined and it would be sad, and wrong, to deprive the user of that information. If people are concerned with the proliferation of GO terms for binding of various substrate, then just have a higher level term for 'substrate binding' and make the existing more specific ones children of that term. <br />
<br />
== Question 3 ==<br />
'''Change the definition of the' x binding' terms to explicitly exclude catalytic domain substrate binding AND make grouping terms for the activity molecular function terms to indicate the type of substrate being chemically changed (e.g. new GO term: 'catalytic activity; ATP hydrolysing')'''<br />
<br />
Comments:<br />
#How is this different from ATPase activity?<br />
#I'm sorry that I'm a bit confused by this. Is this indicating that ATP is being used to drive another reaction. Am I supposed to annotate to this term only if they prove that ATP has been hydrolyzed? If so, it seems like I still would not be able to capture a lot of "incomplete" information when this has not been tested.<br />
#You say "in addition to the benefits associated with proposal 1..." - there were no benefits listed for proposal 1.<br />
#I agree with the cons<br />
#I agree with this suggestion, assuming it is possible<br />
#I am in general in favor of trying to keep track of ATP utilizing enzymes, but am unsure of the best way to do it, nor am I sure that GO is the best place for this.<br />
#The argument proposed by the "cons" seems to me to be applicable to the actual functions (such as enzymatic activities) themselves, irrespective of whether or not you specify the cofactor. When defining enzymatic activities you obviously have to specify (at least in general terms) what the substrate is; this in spite of the clear caveat that all possible substrates have not been exhaustively tested. The same logic could be applied to cofactors: an enzyme could employ either ATP, GTP, both, or indeed other NTPs. Therefore, the use of a hierarchical classification of enzymatic activities or molecular functions should naturally allow the annotator to apply his or her own judgement as to what the appropriate level of specificity should be for the definition of both substrate and cofactor.<br />
#I think this would make the GO terms expand too much... what if the assay was performed with ATP-gamma-S? Would there be a GO term for every substrate tested? This would get out of hand, would it not?<br />
#Not sure how this solves the problem mentioned in comments to question one. That is, one could not annotate to 'catalytic activity; ATP hydrolyzing' if the protein binds ATP but has not been demonstrated to hydrolyze it how will this help? <br />
#difficult to implement.<br />
#Annotate what is shown experimentally only. I agree with the 'con' statement.<br />
<br />
== Question 4 ==<br />
'''Annotate to 'x binding' terms only when a gene product is found either to bind 'x' and not alter it (e.g. as a cofactor) AND when the only information available for a gene product is that they bind 'x.'''<br />
<br />
Comments:<br />
#Annotate based on the experiment, not what happens to the bound substance.<br />
#Do we have to invalidate the old curation once we do find that it hydrolyzes ATP? This was mentioned in the working group document. In a sense, if someone did a search for ATP-binding, what they would really be getting are the "ATP-binding, not further tested or curated + ATP-non-hydrolyzing" group and that doesn't seem ideal.<br />
#Annotate to 'x binding' terms only when a gene product is found to bind 'x'. Period. Inclusion of 'either' with 'AND' in the question is confusing. I think 'OR' is intended.<br />
#As before, annotation of such binding should only be made when the experiment specifically shows such binding, when the point of the experiment is to prove such binding, not inferred by the annotator because of the presence or requirement of a cofactor or reagent in the reaction mix.<br />
#This makes sense: define binding as not including known catalytic activity, and define catalytic activity as including binding. To clean up the old annotations, just search for papers that annotate the same protein to both terms.<br />
#If you are going down the road of remiving substrate binding, then I wonder if perhaps it might not be better to remove cofactors too. Cofactor binding can't be thought of as a molecular function, and in many cases the cofactor requirements are investigated with perhaps less rigour than the substrate specificity. If you did this then you would be reliant on an external classification that stores such information such as the EC classification. <br />
#Again, if we exclude substrate binding, GO terms need to be available for the cofactor or allosteric regulator, but it is not necessary (in my opinion) to further define the exact chemical. Info about the specific type of cofactor or regulator could be put into another column (ie. isn't column 16 for something like this?).<br />
#Seems like this would solve my concerns. If a GTPase has been shown to hydrolyze GTP then, don't need to annotate to GTP binding, however it would, if all that is known is that it binds GTP. We would just need to educate our users that GTP binding is implicit in annotation to GTPase activity. As long as the tree is accurate, then all gene products that bind GTP can be identified.<br />
#difficult to implement: often we do not have enough information (now), but a few months later, everything is different: this would be impossible to implement, and confusing for users. <br />
#I think that the only time you should annotate "x binding" terms is when the only function is "x binding" or when no other information is available. I don't think it is worthwhile to make an exception for non-catalytic binding.<br />
#Too restrictive.<br />
<br />
== Question 5 ==<br />
'''Create two 'x' binding terms: those describing substrate binding interactions and those describing cofactor binding interactions.'''<br />
<br />
Comments:<br />
#I am very naive and I apologize for that. Let's say a transporter binds and hydrolyzes ATP to pump a proton. Although, technically, ATP is certainly a substrate of that transporter, is that what most users would think of as a "substrate" of a transporter? In principle, I like this distinction, but again, I worry that most authors, when showing that protein X binds Y will not tell us whether Y is acting as cofactor or a substrate. In some cases, it might be easy to infer, but, not in all cases. And how would this affect IEA annotations? Do these state whether the bound molecule acts as a cofactor or a substrate?<br />
#I don't think this is necessary.<br />
#Presumably there would be a parent term, e.g. ATP binding, in order for this to work. This would be my second choice if something HAS to change.<br />
#Who needs to be told that GTPase binds GTP?<br />
#Just annotate to what the experiment shows.<br />
#I only agree with this solution if there is a common 'binding' parent e.g. ATP binding ---ATP binding, ATP as substrate ---ATP binding, ATP as cofactor for when you don't know what sort of binding is taking place. I don't see expansion of terms as a problem.<br />
#I think this is too complex. Agree with the "cons" that GO is probably not the best place for such information. <br />
#Quite like this idea but not the idea of retrofitting our annotations - ok if it can all migrate to a common parent for now. <br />
#the same molecule can sometimes be a co-substrate, and at other times a cofactor that is not changed during the reaction. Plus, there are all those enzymes where the mechanism is not known. This distinction would be difficult to implement<br />
#Again, what I would like to avoid is having a specific GO term for every molecule that a gene product binds as a substrate or cofactor. I think there should be one new term for regulated by a small molecule allosteric effector and then put the CHEBI code for the molecule in column 16. <br />
#Can the specific substrate/cofactor not be captured in column 16 with a more generic term (any of the direct children of 'binding') as the GO id?<br />
<br />
== Question 6 ==<br />
'''Create a relationship in the ontology such that if an annotation is made to a catalyst term then we also know that the gene product is annotated to a binding term for the substrates e.g. add a new relationship: 'GTP binding' involved in 'GTPase activity'.''' <br />
<br />
Comments:<br />
#sorry- I'm confused.<br />
#I prefer not to make implied annotations.<br />
#Better to do it by definitions. See comments to #4 above.<br />
#This is complicated, and I am not sure I understand the argument of the cons here. ATP-binding would have a mixed bag of associations - presumably many activities would "point" to ATP-binding - but why is that a problem as it reflects biological reality? <br />
#This choice is made in the opinion that we go all the way and try to solve the 'binding' issue however best we can or else leave things the way they are.<br />
#The usage notes in AmiGO, GONUTS or OboEdit could take care of this... and make it clearer to any annotator that this is implicit.<br />
#Seems like this should be implicit in the catalysis term 'GTPase activity'. As such, as long as the tree is structured correctly, seems obvious that a GTPase has to bind GTP to hydrolyze it. <br />
#In the case of implied annotation, a new evidence code should be used to indicate the relationship/dependency (something similar to IC (inferred by curator) that could be called IR 'inferred by relationship'). In opposite, an explicit annotation would have a 'better' evidence code. <br />
#Yes, this sounds like a good idea, except: how to deal with big complexes that have catalytic, regulatory and structural components, e.g. F0/F1-ATPase. One should not add the term "ATP-binding" to all subunits, but only to those that really bind ATP. This is what is done in UniProt, with regards to the Keyword "ATP-binding".<br />
#What about GTP binding that is NOT involved in GTPase activity? This would create a true path violation.<br />
<br />
== Question 7 ==<br />
'''Do nothing. Allow curators to use the existing terms that describe 'x binding' and accept that the resulting annotations will not indicate to users whether the gene product binds the molecule as a substrate or cofactor.<br />
'''<br />
<br />
Comments:<br />
#Working on extended thoughts will be at http://wiki.geneontology.org/index.php/User:JimHu/Binding_terms<br />
#Please be aware that I am answering this survey based on gut reactions with very few examples at hand and a very limited knowledge of substrate binding matters.<br />
#It is not always straightforward to decide if the molecule is a substrate or cofactor, the author may not give all this information - we would lose a lot of information if we did not annotate these at all. Has the user community been asked about this - I can't see that they would be too perturbed to see that an ATPase had been annotated to ATP binding.<br />
#If GTP binding is documented, it should be annotated. That might lead someone to test whether GTP is a substrate or cofactor. And anyone interested in "in vitro kinetics" or testing or assays would certainly like that information, even if it is only IEA.<br />
#Annotators should annotate the specific data in a paper and resist the temptation to annotate binding events which are not specifically shown in the paper.<br />
#not sure, I could be persuaded to accept this solution<br />
#Reading through this it seems like there's a danger the solution might be worse than the problem!<br />
#One of the arguments advanced is that GO is not the place for substrate/cofactor info. I kind of agree with that though I am still new to GO. Therefore it seems to me that the answer to the part of the question that states "..accept that the resulting annotations will not indicate to users whether the gene product binds the molecule as a substrate or cofactor.." should be "yes" whatever the outcome. GO should not try to indicate whether a molecule is a substrate or a cofactor.<br />
#Though I chose other options above, I am fine with GO being the way it is, but in support of clearly stating the status quo in the documentation. Sometimes I think that if we just represented what the authors show in the paper used in any single annotation, we would be fine. Personally I find that some of the problems arise from curators being ambitious and wanting to provide 'complete information' though this is done with good intentions.<br />
#Clearly, a decision must be made. This has been a stumbling block many times and I think a single choice must be made! <br />
#I'm torn between yes, but modify GO doc and Jim's suggestion. If we 'do nothing' we should at least tidy up the DAG and fill-in/remove some terms. Similar to the random selection of protein complex terms there are a fairly random selection of terms based on what folk could be bothered to ask for. NTRs however efficiently handled so things done. Curators much prefer to get by with what is there than stop to make a new request - this must biase curation significantly. Again we must remember, GO is not the only info captured by many MOD curators.<br />
#The most important point: try and imagine the expectations of GO users and their needs. Try and imagine how they use GO annotation, and with what goals. The "Binding" terms could certainly be improved, by thinking about how they are used, and by adding additional hierarchies. It is important to make GO annotation as user-friendly as possible. It is equally important to consider the practical difficulties associated with annotation, e.g. rapid changes in the amount of available information that would change the status of a GTP-binding protein to GTPase. <br />
#I think the issue can be resolved a) by modifying the documentation and help tips on Amigo to make it clear that binding of a substrate is include in the definition for enzymes and transporters, b) create a GO term for allosteric effector to be used for all effectors and put the CHEBI ID or SwissProt ID in column 16, c) have a policy for whoever is in charge of GO terms that will limit the creation of new binding terms requested for substrate binding, and d) remove GO binding terms that have no genes annotated to them <br />
#Modifying the GO documentation for clarity is always good.</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Binding_Terms_Survey_Comments&diff=20290Binding Terms Survey Comments2009-06-08T13:53:15Z<p>Vpetri: </p>
<hr />
<div>Back to binding terms conference call [http://wiki.geneontology.org/index.php/Binding_Terms_Conference_Call_Information wiki]<br />
<br />
Please note that these comments are added manually and therefore if additional modifications are made to the comments field of the survey please email r.lovering@ucl.ac.uk providing something from the text of the question before modification and the text after so that the new comment can be added below.<br />
== Question 1 ==<br />
'''The GO consortium should remove all annotations which describe catalytic domain substrate binding, associated with catalytic activities or transport proteins, and no longer annotate these interactions.'''<br />
<br />
Comments:<br />
<br />
#Terms should be annotated to binding terms only if there was an experiment that demonstrated binding. There should not be coannotation for substrate binding if an experiment demonstrates catalytic activity. Instead the catalytic annotation should be made. <br />
#I disagree, but one should only annotate to binding if binding is directly demonstrated. <br />
#I dissagree with the proposal. If paper has experiment for a kinase that demonstrates ATP binding, then we should annotate it. There must be an experiment since the annotation would be an IDA. What if an unknown protein is shown to bind DNA; then 5 years later, it is shown to have helicase activity. It would be counterproductive to then have to remove the first annotation.<br />
#Sympathetic to the proposal but still not completely decided. On the wiki page the question was asked: "Are there cases where a user would want to search for gene products that bind a particular substrate but have different molecular functions? " One answer to this springs to mind, the ubiquitin conugating E2 enzymes. Many of these proteins have lost the catalytic function yet nevertheless bind ubiquitin. For instance, hMMS2/UBE2V2 (catalytically inactive) forms a heterodimer with UBC13 (catalytically active). hMMS2/UBE2V2 binds the donor ubiqutin and orients the ubiquitin lys-63 toward the acceptor site in UBC13. In this case we would have to annotate one member of the heterodimer as ubiquitin-binding and the other one as not doing so, as this subunit is also catalytically active. While I think you can justify this, many users would probably find this confusing. Another example are the argonaute proteins, EIF2C1/AGO1 EIF2C2/AGO2, EIF2C3/AGO3 and EIF2C4/AGO4. All 4 of these proteins bind to an siRNA or miRNA, which serves as a guide for complementary mRNAs. In the case of AGO1, 3 and 4, the bound complementary mRNA is subject to translational repression. Therefore for these 3 proteins you would annotate to mRNA binding as the mRNA is not really a substrate and they lack any kind of catalytic activity. AGO2 on the other hand does have a catalytic activity but also acts like AGO1/3/4. For AGO2 the mRNA is either subject to translational repression (when the miRNA exhibits imperfect complementarity), or subject to endonucleolytic cleavage by AGO2 (generally when the complementarity is perfect - see GO:0070551). So AGO2 could be annotated to mRNA binding but only for papers that demonstrated translational repression, not cleavage. Again I think users would probably find this confusing.<br />
#I agree that if there is evidence supporting a catalytic activity then related binding annotations are not useful. However, there are many cases where for example a suspected GTPase has been demonstrated to bind GTP, but has not been shown to catalyze the hydrolysis, in which case it becomes GTP binding or nothing. So I would say my vote is a qualified yes, its a good idea but what would we do in cases like this? <br />
#I like Jim's suggestion of retaining high level binding terms. Realistically, we are not going to have time to revaluate every binding annotation so by moving things to a generic binding term as least we don't lose the functional info and the retrofit is feasible. However, given that we are not set up for col 16 due to database constraints and also our curators are likely resist the additional burden of having to figure out the appropriate chebi IDs, I suspect there will be a loss of info in terms of what the interacting molecules are for new annotations.<br />
#This is entire survey too binary - in principle, I agree we need to limit the scope of the "binding" terms but keep in mind that there are biological functional "binding" functions.<br />
#If i have evidence for GTPase activity, I would annotate it to just that term. Dual annotation doesn't make sense. But if I have evidence, say based on some domain comparison, that the gp has ATP binding domain, then I would annotate to just ATP binding with ISS.<br />
#Annotate at the level of what function is shown in the experiment. If the experiment shows GTPase activity, then annotate to GTPase activity. If it shows GTP binding, then annotate to GTP binding.<br />
<br />
== Question 2 ==<br />
'''Change the definition of 'x binding' terms to explicitly exclude catalytic domain substrate binding.<br />
'''<br />
Comments:<br />
#For all the questions involving x binding redefinition, I am opposed to precomposed terms of the type "x binding"<br />
#Do not change the definition, change annotation practice.<br />
#When I read a paper and they show that it binds GTP, then I would like to be able to curate that fact, especially when I have no other molecular function information to give. The author is unlikely to make any unequivocal statement stating that it binds GTP but definitely doesn't hydrolyze it. And, if I have to go read other papers that do separate experiments which show that it is "NOT" hydrolyzed, can I really use the original reference as my sole source for that annotation? It seems that I have to draw an inference from multiple experiments to know that it does A (binds GTP), but definitely doesn't do B (use it as a substrate). I like to try to limit my annotations to what is directly shown by a particular experiment when possible.<br />
#Again, binding should only be annotated if it is directly demonstrated.<br />
#It would be an ENORMOUS amount of work to go back through annotations to decide whether the term was used 'correctly' or not<br />
#I am not sure removing all of the "incorrect" annotations is necessary. I view it as "redundant information", which should be eliminated because it doesn't add information. <br />
#Annotation of such binding should only be made when the experiment specifically shows such binding, when the point of the experiment is to prove such binding, not inferred by the annotator because of the presence or requirement of a cofactor or reagent in the reaction mix. <br />
#In many older biochemistry papers, binding was used as an indicator that the protein might have catalytic activity on the binding partner. Ex: one step in the purification of a helicase might be a DNA column, but other proteins that bind to the column might not have helicase activity. It would still be useful to capture the DNA binding activity of these proteins even if they are subsequently shown to have catalytic activity on DNA. Also, it's useful to have a sense of history in GO, i.e. what was known when, so that we can see how partial information (DNA binding) might develop into a clearer picture (topoisimerase).<br />
#I agree with all of the cons; I reject all of the pros.<br />
#I don't see why this applies: "In future curators would not be able to annotate proteins for which the only information presented is that they bind 'x' (with no indication of the context of this binding - is it a substrate/cofactor/something else?). " If they bind 'x' then they could be annotated as such. In the future if 'x' is discovered to be a substrate, the previous annotation would have to be removed. <br />
#I dont think it's possible to do annotation if one annotation (x binding) depends on another annotation (here, catalytic activity).<br />
#This seems to me to be more in line with the intentions of GO and I am not sure that losing these types of annotation is really a bad thing in most cases. However there are perhaps specific cases where this could be very confusing for users as described comments on point 1. On the other hand, if the only information available for a protein is that it binds zinc, or a lipid etc, then that is not much information at all and the significance of a paper that publishes only these kinds of results is perhaps questionable. If you have 2 papers and paper 1 shows cholesterol binding and paper 2 demonstrates a role for the protein as a cholesterol transport protein, I would annotate paper 2 and leave paper 1 aside. See also point 3 below.<br />
#On the condition that there were terms for non-substrates (ie cofactors, allosteric regulators, etc). <br />
#See above. Same concerns if this is all that has been experimentally determined.<br />
#I don't think this will work. While we all know that we should read definitions before annotating if you leave the terms in without making this change explicit in the name curators will keep using them incorrectly. Also, what do you do if it isn't clear whether it is a substrate or not? If you don't annotate you lose the 'binding function' info - if you do annotate it may turn out later to be wrong. GO annotation is only one aspect of the data that is captured from a paper - curators simply don't have time to revise old data in the light of new info during routine curation. Once an annotation is made it is likely to stay there for a long time.<br />
#It is often not possible to make the distinction, e.g. because there is insufficient information. It would be paradoxical to annotate "GTP-binding" only when GTP has a regulatory rule. Plus, would be very difficult to implement.<br />
#Given your definition, it doesn't seem like the con "curators would not be able to annotate proteins with limited information" is a valid point, as it would only apply to proteins that contain catalytic domains (which wouldn't fall into the "all we know is that it binds protein" category).<br />
#I don't think i understand the con part! If the only evidence you have is that gpX has a ATP binding domain, then that is all the annotation you can make. gp can bind to ATP for so many reasons, not always for hydrolysis?<br />
#I think that if curators annotate a catalytic substrate to binding that is OK, but I think the practice should be discouraged. I want to slow down the proliferation of binding terms for every possible substrate in the biological realm.<br />
#What if 'catalytic domain substrate' binding is what the assay demonstrates? We'd want to capture that.<br />
#Many times the Km, an important parameter, is determined and it would be sad, and wrong, to deprive the user of that information. If people are concerned with the proliferation of GO terms for binding of various substrate, then just have a higher level term for 'substrate binding' and make the existing more specific ones children of that term. <br />
<br />
== Question 3 ==<br />
'''Change the definition of the' x binding' terms to explicitly exclude catalytic domain substrate binding AND make grouping terms for the activity molecular function terms to indicate the type of substrate being chemically changed (e.g. new GO term: 'catalytic activity; ATP hydrolysing')'''<br />
<br />
Comments:<br />
#How is this different from ATPase activity?<br />
#I'm sorry that I'm a bit confused by this. Is this indicating that ATP is being used to drive another reaction. Am I supposed to annotate to this term only if they prove that ATP has been hydrolyzed? If so, it seems like I still would not be able to capture a lot of "incomplete" information when this has not been tested.<br />
#You say "in addition to the benefits associated with proposal 1..." - there were no benefits listed for proposal 1.<br />
#I agree with the cons<br />
#I agree with this suggestion, assuming it is possible<br />
#I am in general in favor of trying to keep track of ATP utilizing enzymes, but am unsure of the best way to do it, nor am I sure that GO is the best place for this.<br />
#The argument proposed by the "cons" seems to me to be applicable to the actual functions (such as enzymatic activities) themselves, irrespective of whether or not you specify the cofactor. When defining enzymatic activities you obviously have to specify (at least in general terms) what the substrate is; this in spite of the clear caveat that all possible substrates have not been exhaustively tested. The same logic could be applied to cofactors: an enzyme could employ either ATP, GTP, both, or indeed other NTPs. Therefore, the use of a hierarchical classification of enzymatic activities or molecular functions should naturally allow the annotator to apply his or her own judgement as to what the appropriate level of specificity should be for the definition of both substrate and cofactor.<br />
#I think this would make the GO terms expand too much... what if the assay was performed with ATP-gamma-S? Would there be a GO term for every substrate tested? This would get out of hand, would it not?<br />
#Not sure how this solves the problem mentioned in comments to question one. That is, one could not annotate to 'catalytic activity; ATP hydrolyzing' if the protein binds ATP but has not been demonstrated to hydrolyze it how will this help? <br />
#difficult to implement.<br />
#Annotate what is shown experimentally only. I agree with the 'con' statement.<br />
<br />
== Question 4 ==<br />
'''Annotate to 'x binding' terms only when a gene product is found either to bind 'x' and not alter it (e.g. as a cofactor) AND when the only information available for a gene product is that they bind 'x.'''<br />
<br />
Comments:<br />
#Annotate based on the experiment, not what happens to the bound substance.<br />
#Do we have to invalidate the old curation once we do find that it hydrolyzes ATP? This was mentioned in the working group document. In a sense, if someone did a search for ATP-binding, what they would really be getting are the "ATP-binding, not further tested or curated + ATP-non-hydrolyzing" group and that doesn't seem ideal.<br />
#Annotate to 'x binding' terms only when a gene product is found to bind 'x'. Period. Inclusion of 'either' with 'AND' in the question is confusing. I think 'OR' is intended.<br />
#As before, annotation of such binding should only be made when the experiment specifically shows such binding, when the point of the experiment is to prove such binding, not inferred by the annotator because of the presence or requirement of a cofactor or reagent in the reaction mix.<br />
#This makes sense: define binding as not including known catalytic activity, and define catalytic activity as including binding. To clean up the old annotations, just search for papers that annotate the same protein to both terms.<br />
#If you are going down the road of remiving substrate binding, then I wonder if perhaps it might not be better to remove cofactors too. Cofactor binding can't be thought of as a molecular function, and in many cases the cofactor requirements are investigated with perhaps less rigour than the substrate specificity. If you did this then you would be reliant on an external classification that stores such information such as the EC classification. <br />
#Again, if we exclude substrate binding, GO terms need to be available for the cofactor or allosteric regulator, but it is not necessary (in my opinion) to further define the exact chemical. Info about the specific type of cofactor or regulator could be put into another column (ie. isn't column 16 for something like this?).<br />
#Seems like this would solve my concerns. If a GTPase has been shown to hydrolyze GTP then, don't need to annotate to GTP binding, however it would, if all that is known is that it binds GTP. We would just need to educate our users that GTP binding is implicit in annotation to GTPase activity. As long as the tree is accurate, then all gene products that bind GTP can be identified.<br />
#difficult to implement: often we do not have enough information (now), but a few months later, everything is different: this would be impossible to implement, and confusing for users. <br />
#I think that the only time you should annotate "x binding" terms is when the only function is "x binding" or when no other information is available. I don't think it is worthwhile to make an exception for non-catalytic binding.<br />
#Too restrictive.<br />
<br />
== Question 5 ==<br />
'''Create two 'x' binding terms: those describing substrate binding interactions and those describing cofactor binding interactions.'''<br />
<br />
Comments:<br />
#I am very naive and I apologize for that. Let's say a transporter binds and hydrolyzes ATP to pump a proton. Although, technically, ATP is certainly a substrate of that transporter, is that what most users would think of as a "substrate" of a transporter? In principle, I like this distinction, but again, I worry that most authors, when showing that protein X binds Y will not tell us whether Y is acting as cofactor or a substrate. In some cases, it might be easy to infer, but, not in all cases. And how would this affect IEA annotations? Do these state whether the bound molecule acts as a cofactor or a substrate?<br />
#I don't think this is necessary.<br />
#Presumably there would be a parent term, e.g. ATP binding, in order for this to work. This would be my second choice if something HAS to change.<br />
#Who needs to be told that GTPase binds GTP?<br />
#Just annotate to what the experiment shows.<br />
#I only agree with this solution if there is a common 'binding' parent e.g. ATP binding ---ATP binding, ATP as substrate ---ATP binding, ATP as cofactor for when you don't know what sort of binding is taking place. I don't see expansion of terms as a problem.<br />
#I think this is too complex. Agree with the "cons" that GO is probably not the best place for such information. <br />
#Quite like this idea but not the idea of retrofitting our annotations - ok if it can all migrate to a common parent for now. <br />
#the same molecule can sometimes be a co-substrate, and at other times a cofactor that is not changed during the reaction. Plus, there are all those enzymes where the mechanism is not known. This distinction would be difficult to implement<br />
#Again, what I would like to avoid is having a specific GO term for every molecule that a gene product binds as a substrate or cofactor. I think there should be one new term for regulated by a small molecule allosteric effector and then put the CHEBI code for the molecule in column 16. <br />
#Can the specific substrate/cofactor not be captured in column 16 with a more generic term (any of the direct children of 'binding') as the GO id?<br />
<br />
== Question 6 ==<br />
'''Create a relationship in the ontology such that if an annotation is made to a catalyst term then we also know that the gene product is annotated to a binding term for the substrates e.g. add a new relationship: 'GTP binding' involved in 'GTPase activity'.''' <br />
<br />
Comments:<br />
#sorry- I'm confused.<br />
#I prefer not to make implied annotations.<br />
#Better to do it by definitions. See comments to #4 above.<br />
#This is complicated, and I am not sure I understand the argument of the cons here. ATP-binding would have a mixed bag of associations - presumably many activities would "point" to ATP-binding - but why is that a problem as it reflects biological reality? <br />
#This choice is made in the opinion that we go all the way and try to solve the 'binding' issue however best we can or else leave things the way they are.<br />
#The usage notes in AmiGO, GONUTS or OboEdit could take care of this... and make it clearer to any annotator that this is implicit.<br />
#Seems like this should be implicit in the catalysis term 'GTPase activity'. As such, as long as the tree is structured correctly, seems obvious that a GTPase has to bind GTP to hydrolyze it. <br />
#In the case of implied annotation, a new evidence code should be used to indicate the relationship/dependency (something similar to IC (inferred by curator) that could be called IR 'inferred by relationship'). In opposite, an explicit annotation would have a 'better' evidence code. <br />
#Yes, this sounds like a good idea, except: how to deal with big complexes that have catalytic, regulatory and structural components, e.g. F0/F1-ATPase. One should not add the term "ATP-binding" to all subunits, but only to those that really bind ATP. This is what is done in UniProt, with regards to the Keyword "ATP-binding".<br />
#What about GTP binding that is NOT involved in GTPase activity? This would create a true path violation.<br />
<br />
== Question 7 ==<br />
'''Do nothing. Allow curators to use the existing terms that describe 'x binding' and accept that the resulting annotations will not indicate to users whether the gene product binds the molecule as a substrate or cofactor.<br />
'''<br />
<br />
Comments:<br />
#Working on extended thoughts will be at http://wiki.geneontology.org/index.php/User:JimHu/Binding_terms<br />
#Please be aware that I am answering this survey based on gut reactions with very few examples at hand and a very limited knowledge of substrate binding matters.<br />
#It is not always straightforward to decide if the molecule is a substrate or cofactor, the author may not give all this information - we would lose a lot of information if we did not annotate these at all. Has the user community been asked about this - I can't see that they would be too perturbed to see that an ATPase had been annotated to ATP binding.<br />
#If GTP binding is documented, it should be annotated. That might lead someone to test whether GTP is a substrate or cofactor. And anyone interested in "in vitro kinetics" or testing or assays would certainly like that information, even if it is only IEA.<br />
#Annotators should annotate the specific data in a paper and resist the temptation to annotate binding events which are not specifically shown in the paper.<br />
#not sure, I could be persuaded to accept this solution<br />
#Reading through this it seems like there's a danger the solution might be worse than the problem!<br />
#One of the arguments advanced is that GO is not the place for substrate/cofactor info. I kind of agree with that though I am still new to GO. Therefore it seems to me that the answer to the part of the question that states "..accept that the resulting annotations will not indicate to users whether the gene product binds the molecule as a substrate or cofactor.." should be "yes" whatever the outcome. GO should not try to indicate whether a molecule is a substrate or a cofactor.<br />
#Though I chose other options above, I am fine with GO being the way it is, but in support of clearly stating the status quo in the documentation. Sometimes I think that if we just represented what the authors show in the paper used in any single annotation, we would be fine. Personally I find that some of the problems arise from curators being ambitious and wanting to provide 'complete information' though this is done with good intentions.<br />
#Clearly, a decision must be made. This has been a stumbling block many times and I think a single choice must be made! <br />
#I'm torn between yes, but modify GO doc and Jim's suggestion. If we 'do nothing' we should at least tidy up the DAG and fill-in/remove some terms. Similar to the random selection of protein complex terms there are a fairly random selection of terms based on what folk could be bothered to ask for. NTRs however efficiently handled so things done. Curators much prefer to get by with what is there than stop to make a new request - this must biase curation significantly. Again we must remember, GO is not the only info captured by many MOD curators.<br />
#The most important point: try and imagine the expectations of GO users and their needs. Try and imagine how they use GO annotation, and with what goals. The "Binding" terms could certainly be improved, by thinking about how they are used, and by adding additional hierarchies. It is important to make GO annotation as user-friendly as possible. It is equally important to consider the practical difficulties associated with annotation, e.g. rapid changes in the amount of available information that would change the status of a GTP-binding protein to GTPase. <br />
#I think the issue can be resolved a) by modifying the documentation and help tips on Amigo to make it clear that binding of a substrate is include in the definition for enzymes and transporters, b) create a GO term for allosteric effector to be used for all effectors and put the CHEBI ID or SwissProt ID in column 16, c) have a policy for whoever is in charge of GO terms that will limit the creation of new binding terms requested for substrate binding, and d) remove GO binding terms that have no genes annotated to them <br />
#Modifying the GO documentation for clarity is always good.</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Meeting_Progress_Reports_October_2008&diff=16075Meeting Progress Reports October 20082008-10-16T19:15:40Z<p>Vpetri: /* MOD Progress Reports 2008 */</p>
<hr />
<div>===MOD Progress Reports 2008===<br />
<br />
[[Image:link to your document Modname progress report]]<br />
<br />
[[SO progress report for October 2008 meetings]]<br />
<br />
[[Ontology Development progress report for October 2008 meetings]]<br />
<br />
[[MGI Progress Report for October 2008]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15921October 2008 Meeting Logistics2008-10-09T13:56:35Z<p>Vpetri: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 10 people; about 30$ per person.<br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! T-shirt size<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| small<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| medium<br />
| yes<br />
| perhaps<br />
| veggie<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| medium<br />
| yes<br />
| yes<br />
| veggie<br />
| 20 Oct 20:10 United<br />
| 24 Oct 08:40 United<br />
|-<br />
| Michael Ashburner<br />
| large<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| large<br />
| yes<br />
| yes<br />
| yummy<br />
| Oct 20, 5:09PM, UA8185, LGA-Montreal<br />
| Oct 23, 7:55PM, UA8400, Montreal-LGA<br />
|-<br />
| Jennifer Deegan<br />
| medium<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| medium<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| small<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| large<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| large<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| medium<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| x-large<br />
| yes<br />
| yes<br />
| none<br />
|'''Oct 21''', 1031PM, US3162<br />
|(depart by car)<br />
|-<br />
| Mike Cherry<br />
| large<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Judy Blake<br />
| medium<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| large<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| medium<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| x-large<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| medium<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 3:18 p.m. Northwest<br />
|Oct 23, 11:54 a.m. Northwest<br />
|-<br />
| Eurie Hong<br />
| medium<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Julie Park<br />
| medium<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Debby Siegele<br />
| medium<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| medium<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| medium<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| medium<br />
| yes<br />
| no<br />
| none<br />
|Mon, Oct 20, 4:50PM, Continental<br />
|Wed, Oct 22, 5:30PM departure<br />
|-<br />
| Donghui Li<br />
| medium<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| medium<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Edith Wong<br />
| medium<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Amina Abdulla<br />
| small<br />
| yes<br />
| no<br />
| none<br />
| 20th Oct, 8.10pm<br />
| 23rd Oct, 11.55am<br />
|-<br />
| Seth Carbon<br />
| large<br />
| yes<br />
| no<br />
| none<br />
| 20 Oct, from SFO<br />
| 24 Oct, from Montreal<br />
|-<br />
| Candace Collmer<br />
| medium<br />
| yes<br />
| no<br />
| none<br />
|20 Oct 17:15 US Airways<br />
|23 Oct 13:30 US Airways<br />
|-<br />
| Dmitry Sitnikov<br />
| medium<br />
| yes<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Michelle Gwinn Giglio<br />
| medium<br />
|yes<br />
|no<br />
|none<br />
|Oct. 20 6:28 PM United<br />
|Oct. 23 2:23 PM United<br />
|-<br />
| Peter D'Eustachio<br />
| medium<br />
| yes<br />
| no<br />
| none<br />
| <br />
|<br />
|-<br />
|Ingrid Keseler<br />
| medium<br />
|yes<br />
|no<br />
|none<br />
|Oct. 20 6:35 PM Continental<br />
|<br />
|-<br />
| Linda Hannick<br />
| medium<br />
| no<br />
| no<br />
| <br />
|<br />
|<br />
|-<br />
| Pankaj Jaiswal<br />
| large<br />
| no<br />
| no<br />
| <br />
|<br />
|<br />
|-<br />
| Karen Christie<br />
| large<br />
| no<br />
| no<br />
| <br />
|<br />
|<br />
|-<br />
|Li Ni<br />
|small<br />
|no<br />
|no<br />
| <br />
|<br />
|<br />
|-<br />
| Ben Hitz<br />
| xtra-large<br />
| no<br />
| no<br />
|<br />
|<br />
| <br />
|-<br />
|Rama Balakrishnan<br />
|Large<br />
|no<br />
|no<br />
|<br />
|<br />
|<br />
|-<br />
|Rob Nash<br />
|XXL<br />
|no<br />
|no<br />
|<br />
|<br />
|<br />
|-<br />
|Mike Livstone<br />
|XXL<br />
|no<br />
|no<br />
|<br />
|<br />
|<br />
|-<br />
|Stacia Engel<br />
|M<br />
|no<br />
|no<br />
|<br />
|<br />
|<br />
|-<br />
|Val Wood<br />
|S<br />
|no<br />
|no<br />
|<br />
|<br />
|<br />
|-<br />
|Susan Tweedie<br />
|M<br />
|yes<br />
|<br />
|none<br />
|<br />
|<br />
|-<br />
|Rachael Huntley<br />
|Medium<br />
|no<br />
|no<br />
|<br />
|<br />
|-<br />
|Ruth Lovering<br />
|M<br />
|no<br />
|no<br />
|<br />
|<br />
|<br />
|-<br />
|Rachael Huntley<br />
|Medium<br />
|no<br />
|no<br />
|<br />
|<br />
|<br />
|-<br />
|Emily Dimmer<br />
|Medium<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Dan Barrell<br />
|Large<br />
|yes<br />
|no<br />
|none<br />
|Oct 20, 1945 BA-95<br />
|Oct 26, 2045 BA-94<br />
|-<br />
|Petra Fey<br />
|Small<br />
|yes<br />
|no<br />
|veggie<br />
|Oct 20, 6:00 PM AA<br />
|Oct 22, 6:35 PM AA<br />
|-<br />
|Scott Durkin<br />
|XXL<br />
|yes<br />
|no<br />
|none<br />
|Oct. 20 6:28 PM United<br />
|Oct. 23 6:00 AM United<br />
|-<br />
|Varsha Khodiyar<br />
|Small<br />
|no<br />
|no<br />
|<br />
|<br />
|-<br />
|Ramana Madupu<br />
|medium<br />
|yes<br />
|no<br />
|veggie<br />
|Oct. 20 6:28 PM United<br />
|Oct. 23 6:00 AM Air Canada<br />
|-<br />
-<br />
}<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15437October 2008 Meeting Logistics2008-09-22T16:27:07Z<p>Vpetri: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
| yummy<br />
| Oct 20, 5:09PM, UA8185, LGA-Montreal<br />
| Oct 23, 7:55PM, UA8400, Montreal-LGA<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 3:18 p.m. Northwest<br />
|Oct 24, 11:54 a.m. Northwest<br />
|-<br />
| Eurie Hong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Julie Park<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Debby Siegele<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| yes<br />
| no<br />
| none<br />
|Mon, Oct 20, 4:50PM, Continental<br />
|Wed, Oct 22, 5:30PM departure<br />
|-<br />
| Donghui Li<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Edith Wong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Amina Abdulla<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Seth Carbon<br />
| yes<br />
| no<br />
| none<br />
| 20 Oct, from SFO<br />
| 24 Oct, from Montreal<br />
|-<br />
| Candace Collmer<br />
| yes<br />
| no<br />
| none<br />
|20 Oct 17:15 US Airways<br />
|23 Oct 13:30 US Airways<br />
|-<br />
| Dmitry Sitnikov<br />
| yes<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Michelle Gwinn Giglio<br />
|yes<br />
|no<br />
|none<br />
|Oct. 20 6:28 PM United<br />
|Oct. 23 2:23 PM United<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| yes<br />
| no<br />
| none<br />
| <br />
| <br />
|}<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15254October 2008 Meeting Logistics2008-09-08T14:18:38Z<p>Vpetri: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
| yummy<br />
| Oct 20, 5:09PM, UA8185, LGA-Montreal<br />
| Oct 23, 7:55PM, UA8400, Montreal-LGA<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Eurie Hong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Julie Park<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Debby Siegele<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| yes<br />
| no<br />
| none<br />
|Mon, Oct 20, 4:50PM, Continental<br />
|Wed, Oct 22, 5:30PM departure<br />
|-<br />
| Donghui Li<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Edith Wong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Amina Abdulla<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Seth Carbon<br />
| yes<br />
| no<br />
| none<br />
| 20 Oct, from SFO<br />
| 24 Oct, from Montreal<br />
|-<br />
| Candace Collmer<br />
| yes<br />
| no<br />
| none<br />
|20 Oct 17:15 US Airways<br />
|23 Oct 13:30 US Airways<br />
|-<br />
| Dmitry Sitnikov<br />
| yes<br />
|<br />
|<br />
|}<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=14802October 2008 Meeting Logistics2008-08-11T15:35:31Z<p>Vpetri: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|-<br />
| Doug Howe<br />
| yes<br />
|<br />
|<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|-<br />
| Victoria Petri<br />
| yes<br />
|<br />
| none<br />
|}<br />
<br />
<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=GO_Field_Trip&diff=12145GO Field Trip2008-03-27T14:23:14Z<p>Vpetri: </p>
<hr />
<div>A field trip is planned to Antelope Island Monday afternoon for bird watching and photography.<br />
The island is about a 45 minute drive from the university and accessed via a causeway. You can tour the farm. This was a working sheep farm and ranch until (I think) about the 1950s. <br />
<br />
[[http://stateparks.utah.gov/parks/antelope-island/]] Official site<br />
<br />
[[http://en.wikipedia.org/wiki/Antelope_Island]] - wikipedia site<br />
<br />
The island has interesting geology, migrating birds pass by and there is a herd of buffalo wandering about. The colors of the island seem different to any other place. <br />
<br />
If this sounds like something you want to do, sign up so we can figure out how to get you all there.<br />
<br />
Sign up list:<br />
<br />
#Judy Blake<br />
#Susan Tweedie<br />
#Stacia Engel<br />
#Harold Drabkin<br />
#Mary Dolan<br />
#Doug Howe<br />
#Victoria Petri</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Register&diff=11689Register2008-02-28T21:02:09Z<p>Vpetri: </p>
<hr />
<div>===Registration for April 2008 GO Meetings at University of Utah, SLC===<br />
<br />
Please register here giving information about which meetings you will be attending. <br />
We are asking for 'years on the project' because this is the 10th year of the GOC and we want to celebrate.<br />
<br />
{|border="1" cell spacing="0" cellpadding="5" align="left"<br />
!Name <br />
!Institution <br />
!Model Organism(s) and/or Speciality <br />
!Years on GOC project <br />
!Role on GOC project <br />
!Coming to Ref Genome? <br />
!Coming to GOC? <br />
!Where are you staying? <br />
!food requirement<br />
|-<br />
|Sue Rhee<br />
|The Arabidopsis Information Resource (TAIR)<br />
|Arabidopsis<br />
|8 years<br />
|Co-PI<br />
|No<br />
|Yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Karen Eilbeck<br />
|University of Utah<br />
|Sequences<br />
|5 years<br />
|SO manager<br />
|yes<br />
|yes<br />
|Home<br />
|veggie<br />
|-<br />
|Judy Blake<br />
|The Jackson Laboratory<br />
|mouse /genomics<br />
|10 years<br />
|PI <br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Suzanna Lewis<br />
|Lawrence Berkeley National Laboratory<br />
|Bioinformatics / fly<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|?<br />
|<br />
|-<br />
|Harold Drabkin<br />
|The Jackson Laboratory<br />
|mouse / biochemistry<br />
|7 years<br />
|BioCurator<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Amelia Ireland<br />
|GO Editorial Office, EBI<br />
|Jack of all trades<br />
|6<br />
|Senior GO Curator<br />
|yes<br />
|yes<br />
|hopefully not on the streets<br />
|<br />
|-<br />
|Jennifer Deegan<br />
|GO Editorial Office, EBI<br />
|Large scale content efforts. <br />
|5 years<br />
|Ontology Editor, Outreach/Advocacy Manager<br />
|No<br />
|Yes<br />
|Little America<br />
|No restrictions<br />
|-<br />
|Daniel Barrell<br />
|EMBL - The EBI<br />
|UniProt/Human/Chicken/Cow<br />
|7 years<br />
|GOA database programmer<br />
|No<br />
|Yes<br />
|Little America<br />
|none<br />
|-|<br />
|David Hill<br />
|The Jackson Laboratory<br />
|mouse/developmental biology/ontology content<br />
|9 years<br />
|MGI curator/ Ontology Development Co-manager<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Midori Harris<br />
|GO Editorial Office, EBI<br />
|GO content, especially trying to keep up with ordinary SourceForge submissions<br />
|9.5 years<br />
|GO Editor; ontology development co-manager<br />
|yes<br />
|yes<br />
|University Guest House<br />
|no restrictions<br />
|-<br />
|Pascale Gaudet<br />
|Northwestern University<br />
|dictyBase curator<br />
|5 years<br />
|annotation/reference genomes/ontology content/AmiGO-WPWG<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Tanya Berardini<br />
|The Arabidopsis Information Resource<br />
|Arabidopsis/developmental biology/ontology content<br />
|6 years<br />
|annotation/reference genomes/ontology development/OBO-Edit working group/annotation outreach<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Mary Dolan<br />
|MGI, The Jackson Laboratory<br />
|Mouse<br />
|5 years<br />
|computational methods/tool development/software<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|none<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5 years<br />
|curator/user advocacy (gohelp)/software development for semi-automated curation<br />
|yes<br />
|yes<br />
|University Guest House<br />
|none<br />
|-<br />
|Mike Cherry<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|none<br />
|-<br />
|Doug Howe<br />
|ZFIN, U. Oregon<br />
|D. rerio<br />
|4.5 years<br />
|Ontology development/Ref. Genome/GO annotation<br />
|Yes<br />
|Yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Stacia Engel<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|6 years<br />
|Curator/refGenome<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|<br />
|-<br />
|Susan Tweedie<br />
|FlyBase, University of Cambridge<br />
|Drosophila<br />
|2 years<br />
|GO annotation/ref. genome/newsletter team<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
|-<br />
|Seth Carbon<br />
|Berkeley BOP<br />
|AmiGO/Software<br />
|~1 1/2<br />
|AmiGO/Software and related WGs<br />
|yes<br />
|yes<br />
|TBD<br />
|none<br />
|-<br />
| Valerie Wood<br />
| WT Sanger Institute<br />
| S. pombe MOD DB project manager<br />
| 8<br />
| S. pombe / GO curator/ ref genomes group/ AWG (retired!)<br />
| yes<br />
| yes<br />
| TBD <br />
|<br />
|-<br />
|Fiona McCarthy <br />
|Mississipi State University (AgBase)<br />
|chicken & cow <br />
|3 sort of<br />
|associate GOC member, chick Ref genome, Outreach<br />
|yes <br />
|yes<br />
|TBD<br />
|<br />
|-<br />
|Ranjana Kishore<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5<br />
|Curator/Annotation, Ref genomes, Outreach<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
<br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
|<br />
|8<br />
|Software Manager<br />
|yes<br />
|yes<br />
|?<br />
|veggie<br />
|-<br />
|Donghui Li<br />
|TAIR<br />
|Arabidopsis/ontology content<br />
|2 years<br />
|annotation/reference genomes/ontology development<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|veggie<br />
|-<br />
|Emily Dimmer<br />
|GOA<br />
|Human<br />
|4.5 years<br />
|curator/GOA co-ordinator<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Jim Hu<br />
|EcoliWiki/EcoliHub and GONUTS<br />
|''E. coli''<br />
|1.5 years<br />
|E. coli for RefGenome<br />
|yes<br />
|no (have to teach)<br />
| University Guesthouse<br />
|Lac<sup>-</sup><br />
|-<br />
|Debby Siegele<br />
|EcoliWiki/EcoliHub<br />
|''E. coli''<br />
|1 year<br />
|E. coli for RefGenome<br />
|yes<br />
|no<br />
| University Guesthouse<br />
|<br />
|-<br />
|Rex Chisholm<br />
|dictyBase<br />
|D. discoideum<br />
|9 years<br />
|co-PI/reference genomes<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|<br />
|-<br />
|Michelle Gwinn Giglio<br />
|Institute for Genome Sciences<br />
|prokaryotes<br />
|7 years<br />
|annotator/term developer/PAMGO/outreach group/evidence group<br />
|no<br />
|yes<br />
|University Guest House<br />
|<br />
|-<br />
|Victoria Petri<br />
|Rat Genome Database<br />
|rat / biochemistry<br />
|4.5 years<br />
|GO annotations/Ref. Genomes/Newsletter team/Term contributions<br />
|yes<br />
|yes<br />
|University Guest House<br />
|none<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
<br />
<br />
[[SLC_GO_Consortium_Meeting|SLC Consortium meeting]] |<br />
[[SLC_GO_Reference_Genome_Project_Meeting|SLC Ref Genomes meeting]] | [[GO_Field_Trip|SLC field trip]] |<br />
[[Consortium_Meetings|Consortium meetings main page]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Register&diff=11688Register2008-02-28T20:57:43Z<p>Vpetri: </p>
<hr />
<div>===Registration for April 2008 GO Meetings at University of Utah, SLC===<br />
<br />
Please register here giving information about which meetings you will be attending. <br />
We are asking for 'years on the project' because this is the 10th year of the GOC and we want to celebrate.<br />
<br />
{|border="1" cell spacing="0" cellpadding="5" align="left"<br />
!Name <br />
!Institution <br />
!Model Organism(s) and/or Speciality <br />
!Years on GOC project <br />
!Role on GOC project <br />
!Coming to Ref Genome? <br />
!Coming to GOC? <br />
!Where are you staying? <br />
!food requirement<br />
|-<br />
|Sue Rhee<br />
|The Arabidopsis Information Resource (TAIR)<br />
|Arabidopsis<br />
|8 years<br />
|Co-PI<br />
|No<br />
|Yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Karen Eilbeck<br />
|University of Utah<br />
|Sequences<br />
|5 years<br />
|SO manager<br />
|yes<br />
|yes<br />
|Home<br />
|veggie<br />
|-<br />
|Judy Blake<br />
|The Jackson Laboratory<br />
|mouse /genomics<br />
|10 years<br />
|PI <br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Suzanna Lewis<br />
|Lawrence Berkeley National Laboratory<br />
|Bioinformatics / fly<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|?<br />
|<br />
|-<br />
|Harold Drabkin<br />
|The Jackson Laboratory<br />
|mouse / biochemistry<br />
|7 years<br />
|BioCurator<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Amelia Ireland<br />
|GO Editorial Office, EBI<br />
|Jack of all trades<br />
|6<br />
|Senior GO Curator<br />
|yes<br />
|yes<br />
|hopefully not on the streets<br />
|<br />
|-<br />
|Jennifer Deegan<br />
|GO Editorial Office, EBI<br />
|Large scale content efforts. <br />
|5 years<br />
|Ontology Editor, Outreach/Advocacy Manager<br />
|No<br />
|Yes<br />
|Little America<br />
|No restrictions<br />
|-<br />
|Daniel Barrell<br />
|EMBL - The EBI<br />
|UniProt/Human/Chicken/Cow<br />
|7 years<br />
|GOA database programmer<br />
|No<br />
|Yes<br />
|Little America<br />
|none<br />
|-|<br />
|David Hill<br />
|The Jackson Laboratory<br />
|mouse/developmental biology/ontology content<br />
|9 years<br />
|MGI curator/ Ontology Development Co-manager<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Midori Harris<br />
|GO Editorial Office, EBI<br />
|GO content, especially trying to keep up with ordinary SourceForge submissions<br />
|9.5 years<br />
|GO Editor; ontology development co-manager<br />
|yes<br />
|yes<br />
|University Guest House<br />
|no restrictions<br />
|-<br />
|Pascale Gaudet<br />
|Northwestern University<br />
|dictyBase curator<br />
|5 years<br />
|annotation/reference genomes/ontology content/AmiGO-WPWG<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Tanya Berardini<br />
|The Arabidopsis Information Resource<br />
|Arabidopsis/developmental biology/ontology content<br />
|6 years<br />
|annotation/reference genomes/ontology development/OBO-Edit working group/annotation outreach<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Mary Dolan<br />
|MGI, The Jackson Laboratory<br />
|Mouse<br />
|5 years<br />
|computational methods/tool development/software<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|none<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5 years<br />
|curator/user advocacy (gohelp)/software development for semi-automated curation<br />
|yes<br />
|yes<br />
|University Guest House<br />
|none<br />
|-<br />
|Mike Cherry<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|none<br />
|-<br />
|Doug Howe<br />
|ZFIN, U. Oregon<br />
|D. rerio<br />
|4.5 years<br />
|Ontology development/Ref. Genome/GO annotation<br />
|Yes<br />
|Yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Stacia Engel<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|6 years<br />
|Curator/refGenome<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|<br />
|-<br />
|Susan Tweedie<br />
|FlyBase, University of Cambridge<br />
|Drosophila<br />
|2 years<br />
|GO annotation/ref. genome/newsletter team<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
|-<br />
|Seth Carbon<br />
|Berkeley BOP<br />
|AmiGO/Software<br />
|~1 1/2<br />
|AmiGO/Software and related WGs<br />
|yes<br />
|yes<br />
|TBD<br />
|none<br />
|-<br />
| Valerie Wood<br />
| WT Sanger Institute<br />
| S. pombe MOD DB project manager<br />
| 8<br />
| S. pombe / GO curator/ ref genomes group/ AWG (retired!)<br />
| yes<br />
| yes<br />
| TBD <br />
|<br />
|-<br />
|Fiona McCarthy <br />
|Mississipi State University (AgBase)<br />
|chicken & cow <br />
|3 sort of<br />
|associate GOC member, chick Ref genome, Outreach<br />
|yes <br />
|yes<br />
|TBD<br />
|<br />
|-<br />
|Ranjana Kishore<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5<br />
|Curator/Annotation, Ref genomes, Outreach<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
<br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
|<br />
|8<br />
|Software Manager<br />
|yes<br />
|yes<br />
|?<br />
|veggie<br />
|-<br />
|Donghui Li<br />
|TAIR<br />
|Arabidopsis/ontology content<br />
|2 years<br />
|annotation/reference genomes/ontology development<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|veggie<br />
|-<br />
|Emily Dimmer<br />
|GOA<br />
|Human<br />
|4.5 years<br />
|curator/GOA co-ordinator<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Jim Hu<br />
|EcoliWiki/EcoliHub and GONUTS<br />
|''E. coli''<br />
|1.5 years<br />
|E. coli for RefGenome<br />
|yes<br />
|no (have to teach)<br />
| University Guesthouse<br />
|Lac<sup>-</sup><br />
|-<br />
|Debby Siegele<br />
|EcoliWiki/EcoliHub<br />
|''E. coli''<br />
|1 year<br />
|E. coli for RefGenome<br />
|yes<br />
|no<br />
| University Guesthouse<br />
|<br />
|-<br />
|Rex Chisholm<br />
|dictyBase<br />
|D. discoideum<br />
|9 years<br />
|co-PI/reference genomes<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|<br />
|-<br />
|Michelle Gwinn Giglio<br />
|Institute for Genome Sciences<br />
|prokaryotes<br />
|7 years<br />
|annotator/term developer/PAMGO/outreach group/evidence group<br />
|no<br />
|yes<br />
|University Guest House<br />
|<br />
|-<br />
|Victoria Petri<br />
|Rat Genome Database<br />
|rat / biochemistry<br />
|GO annotations/Ref. Genomes/Newsletter team/Term contributions<br />
|4.5 years<br />
|yes<br />
|yes<br />
|University Guest House<br />
|none<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
<br />
<br />
[[SLC_GO_Consortium_Meeting|SLC Consortium meeting]] |<br />
[[SLC_GO_Reference_Genome_Project_Meeting|SLC Ref Genomes meeting]] | [[GO_Field_Trip|SLC field trip]] |<br />
[[Consortium_Meetings|Consortium meetings main page]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Future_newsletter_items&diff=8242Future newsletter items2008-02-11T19:45:18Z<p>Vpetri: /* Items for February newsletter */</p>
<hr />
<div>==Items for February newsletter==<br />
<br />
* Announcement of new disjoint_from tags in gene_ontology.obo file (Jane)<br />
** also mention that SO has them now too between the top nodes and between region and junction<br />
<br />
* SGD gene_assocations file will now have IEAs beginning March 8th (Eurie)<br />
<br />
* Ontology development<br />
** The new regulation relationships (Tanya and David)<br />
** Other developments (topics addressed/done in January?)<br />
<br />
* Orthology establishment for the Reference Genomes MODs genes - Princeton group (for future newsletters)<br />
<br />
* Branching of ISS evidence code - note the the previous letter had an update on evidence codes mentioning that documentation for ISS is 'under review' and now we can announce that this has been completed (Michelle)<br />
<br />
* AmiGO release likely by Feb 20th. Announcement about the new features- AmiGO /Webpresence WG<br />
<br />
*The annotation workshop that Linda Hannick is running.<br />
<br />
==Items for future newsletters==<br />
<br />
<br />
<br />
==Items suggested for newsletters, but better somewhere else==<br />
<br />
* Standards for GO data in publications<br />
<br />
==New task for Group==<br />
* Obtain an ISSN for the Newsletter,[http://www.loc.gov/issn/issnbro.html#how]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Future_newsletter_items&diff=8238Future newsletter items2008-02-05T16:56:23Z<p>Vpetri: /* Items for February newsletter */</p>
<hr />
<div>==Items for February newsletter==<br />
<br />
* Announcement of new disjoint_from tags in gene_ontology.obo file (Jane)<br />
** also mention that SO has them now too between the top nodes and between region and junction<br />
<br />
* SGD gene_assocations file will now have IEAs beginning March 8th (Eurie)<br />
<br />
* Ontology development<br />
** The new regulation relationships<br />
** Other developments (topics addressed/done in January?)<br />
<br />
* Orthology establishment for the Reference Genomes MODs genes - Princeton group<br />
<br />
* Branching of ISS evidence code - note the the previous letter had an update on evidence codes mentioning that documentation for ISS is 'under review' and now we can announce that this has been completed<br />
<br />
==Items for future newsletters==<br />
<br />
The annotation workshop that Linda Hannick is running. (TIGR as was.)<br />
<br />
<br />
==Items suggested for newsletters, but better somewhere else==<br />
<br />
* Standards for GO data in publications<br />
<br />
==New task for Group==<br />
* Obtain an ISSN for the Newsletter,[http://www.loc.gov/issn/issnbro.html#how]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Future_newsletter_items&diff=8237Future newsletter items2008-02-05T16:51:51Z<p>Vpetri: /* Items for February newsletter */</p>
<hr />
<div>==Items for February newsletter==<br />
<br />
* Announcement of new disjoint_from tags in gene_ontology.obo file (Jane)<br />
** also mention that SO has them now too between the top nodes and between region and junction<br />
<br />
* SGD gene_assocations file will now have IEAs beginning March 8th (Eurie)<br />
<br />
* Ontology development<br />
** The new regulation relationships<br />
** Other developments (topics addressed/done in January?)<br />
<br />
* Orthology establishment for the Reference Genomes MODs genes - Princeton group<br />
<br />
==Items for future newsletters==<br />
<br />
The annotation workshop that Linda Hannick is running. (TIGR as was.)<br />
<br />
<br />
==Items suggested for newsletters, but better somewhere else==<br />
<br />
* Standards for GO data in publications<br />
<br />
==New task for Group==<br />
* Obtain an ISSN for the Newsletter,[http://www.loc.gov/issn/issnbro.html#how]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Variant_annotation&diff=10469Variant annotation2007-11-12T23:32:23Z<p>Vpetri: /* Rattus norvegicus */</p>
<hr />
<div>==Arabidopsis thaliana==<br />
==Caenorhabditis elegans==<br />
==Danio rerio==<br />
We almost never have enough info to curate to the level of a splice variant. Our annotations are applied at the level of the gene.<br />
<br />
==Dictyostelium discoideum==<br />
<br />
So far we only have a few genes and publications that described splice variants, and the papers never described different functions for the different variants. Hence, we currently don't capture annotations to different variants of gene products.<br />
<br />
==Drosophila melanogaster==<br />
==Escherichia coli==<br />
==Gallus gallus==<br />
We are using UniProtKB accession IDs wherever possible and this allows us to annotate specific isoforms if required.<br />
<br />
==Homo sapiens==<br />
<br />
The human group annotates to UniProtKB accessions. When a paper provides isoform-specific information, then this data can be captured using the appropriate UniProt isoid. E.g. Q4VCS5-1, Q4VCS5-2.<br />
When isoform-specific information is not provided then the top-level UniProt accession number is only annotated to, e.g. Q4VCS5.<br />
<br />
==Mus musculus==<br />
For each annotation, MGI has a "notes field" that is not available to the public. That note has a structure as follows:<br />
<br />
evidence:<br />
anatomy:<br />
cell type:<br />
gene product:<br />
qualifier:<br />
target:<br />
external ref:<br />
text:<br />
<br />
If a paper actually specifies a specific isoform, the appropriate refseq is entered into the "gene_product" field<br />
<br />
eg, For the annotation of MGI:1341722,Kcnh2,to GO:0005886, plasma membrane,by IDA, the field would look like:<br />
<br />
gene_product:SPKW:O35219-1<br />
<br />
We presently only have about 300 of these with experimental evidence codes, annotated after the adoption of the structured notes. So QC has to be done for some. Annotations done prior to that will not have any entry, as we had no way of capturing the data.<br />
We are looking at ways to "back annotate" by identifying having multiple isoforms identified in references that have been used for GO annotation at MGI.<br />
<br />
==Rattus norvegicus==<br />
<br />
There are not too many splice variants currently in the database. Those that are have their own DB:ID, get the symbol of the parent gene with underscore vnumber followed by variant of symbol in parentheses with symbol hyperlinked to the report page of the parent gene. Example:geneX_v1 (variant of geneX). The variants can also be accessed from the top level gene. The variants may have some mapping, sequence, other external database links, if applicable. They seldom have annotations. It may happen that the information in the literature allows for annotation of the splice variants but that is rather rare.<br />
<br />
==Saccharomyces cerevisiae==<br />
==Schizosaccharomyces pombe==</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Variant_annotation&diff=10468Variant annotation2007-11-12T23:30:52Z<p>Vpetri: /* Rattus norvegicus */</p>
<hr />
<div>==Arabidopsis thaliana==<br />
==Caenorhabditis elegans==<br />
==Danio rerio==<br />
We almost never have enough info to curate to the level of a splice variant. Our annotations are applied at the level of the gene.<br />
<br />
==Dictyostelium discoideum==<br />
<br />
So far we only have a few genes and publications that described splice variants, and the papers never described different functions for the different variants. Hence, we currently don't capture annotations to different variants of gene products.<br />
<br />
==Drosophila melanogaster==<br />
==Escherichia coli==<br />
==Gallus gallus==<br />
We are using UniProtKB accession IDs wherever possible and this allows us to annotate specific isoforms if required.<br />
<br />
==Homo sapiens==<br />
<br />
The human group annotates to UniProtKB accessions. When a paper provides isoform-specific information, then this data can be captured using the appropriate UniProt isoid. E.g. Q4VCS5-1, Q4VCS5-2.<br />
When isoform-specific information is not provided then the top-level UniProt accession number is only annotated to, e.g. Q4VCS5.<br />
<br />
==Mus musculus==<br />
For each annotation, MGI has a "notes field" that is not available to the public. That note has a structure as follows:<br />
<br />
evidence:<br />
anatomy:<br />
cell type:<br />
gene product:<br />
qualifier:<br />
target:<br />
external ref:<br />
text:<br />
<br />
If a paper actually specifies a specific isoform, the appropriate refseq is entered into the "gene_product" field<br />
<br />
eg, For the annotation of MGI:1341722,Kcnh2,to GO:0005886, plasma membrane,by IDA, the field would look like:<br />
<br />
gene_product:SPKW:O35219-1<br />
<br />
We presently only have about 300 of these with experimental evidence codes, annotated after the adoption of the structured notes. So QC has to be done for some. Annotations done prior to that will not have any entry, as we had no way of capturing the data.<br />
We are looking at ways to "back annotate" by identifying having multiple isoforms identified in references that have been used for GO annotation at MGI.<br />
<br />
==Rattus norvegicus==<br />
<br />
There are not too many splice variants currently in the database. Those that are have their own DB:ID, get the symbol of the generic gene with underscore vnumber followed by variant of symbol in parentheses with symbol hyperlinked to the report page of the parent gene. Example:geneX_v1 (variant of geneX). The variants can also be accessed from the top level gene. The variants may have some mapping, sequence, other external database links, if applicable. They seldom have annotations. It may happen that the information in the literature allows for annotation of the splice variants but that is rather rare.<br />
<br />
==Saccharomyces cerevisiae==<br />
==Schizosaccharomyces pombe==</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Reference_Genome_sequence_annotation_(Retired)&diff=4331Reference Genome sequence annotation (Retired)2007-11-12T17:41:36Z<p>Vpetri: /* Nota bene */</p>
<hr />
<div>The Reference Genome initiative will foster [http://www.sequenceontology.org SO] compliant annotations. The sequences will be available using the file format [http://www.sequenceontology.org/gff3.shtml GFF3].<br />
<br />
For discussion on standardizing URLs for accessing this information please see the GMOD wiki page <br />
[http://www.gmod.org/wiki/index.php/Standard_URL Standard URL]<br />
<br />
{| border="1"<br />
|+align="bottom" style="color:#e76700;"|''Where to find SO compliant GFF3 annotations for the Reference Genome sequences. ( * means that the presented file is not yet SO compliant)''<br />
|'''Organism'''<br />
|'''Organization'''<br />
|'''Download'''<br />
|'''Date'''<br />
|-<br />
|Drosophila melanogaster (Fruitfly)<br />
|[http://www.flybase.org FlyBase]<br />
|ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff <br />
|9/12/07<br />
|-<br />
|Caenorhabditis elegans (Worm)<br />
|[http://www.wormbase.org WormBase]<br />
|ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3<br />
|?<br />
|-<br />
|Saccharomyces cerevisiae (Budding yeast)<br />
|[http://www.yeastgenome.org SGD]<br />
|ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff<br />
|?<br />
|-<br />
|Dictyostelium (cellular slime mold)<br />
|[http://www.dictybase.org dictyBase]<br />
|http://www.dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=gff3&ID=dicty_gff3.zip<br />
|updated weekly<br />
|-<br />
|Arabidopsis thaliana<br />
|[http://www.arabidopsis.org/ TAIR]<br />
|ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR7_genome_release/TAIR7_gff3<br />
|8/15/07<br />
|-<br />
|Danio rerio (Zebrafish)<br />
|[http://zfin.org ZFIN] [http://www.sanger.ac.uk Sanger Institute]<br />
|Vega: ftp://ftp.sanger.ac.uk/pub/vega/danio/gff3/vega_danio_rerio_20070803.gff3 <br> Ensembl*: ftp://ftp.ensembl.org/pub/current_gtf/Danio_rerio.ZFISH7.47.gtf.gz<br />
|With new releases<br />
|-<br />
|Mouse<br />
|[http://www.informatics.jax.org/ MGI]<br />
|? <br />
|?<br />
|-<br />
|Human<br />
|[http://www.ebi.ac.uk/GOA/ GOA]<br />
| ftp://ftp.ensembl.org/pub/current_gtf/Homo_sapiens.NCBI36.47.gtf.gz<br />
|?<br />
|-<br />
|Schizosaccharomyces pombe (Fission yeast)<br />
|[http://www.sanger.ac.uk/Projects/S_pombe/ Sanger Centre]<br />
| * ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/<br />
|3/16/07<br />
|-<br />
|E.coli<br />
|[http://asap.ahabs.wisc.edi ASAP]<br />
|https://asap.ahabs.wisc.edu/asap/download_gff3.php?LocationID=&SequenceVersionID=&GenomeID=<br />
|?<br />
|-<br />
|Rat<br />
|[http://rgd.mcw.edu/ RGD]<br />
|ftp://ftp.ensembl.org/pub/current_gtf/Rattus_norvegicus.RGSC3.4.47.gtf.gz<br />
|?<br />
|-<br />
|}<br />
<br />
== Nota bene ==<br />
# The human and zebrafish Ensembl data is in GTF (not GFF3)<br />
# The rat Ensembl data (link provided) is also in GTF format<br />
# The pombe files are not (yet) valid GFF3. The known problems are:<br />
#* extra column 10 "Name"<br />
#* extra column 11 "orf_classification"<br />
#* extra column 12 "gene"<br />
#* extra column 13 "chr"<br />
#* the mandatory "phase" column isn't filled in.<br />
#* and the attributes" column may not be formatted correctly.<br />
<br />
Back to: [[Reference_Genome_Focus]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Reference_Genome_sequence_annotation_(Retired)&diff=4330Reference Genome sequence annotation (Retired)2007-11-12T17:39:42Z<p>Vpetri: </p>
<hr />
<div>The Reference Genome initiative will foster [http://www.sequenceontology.org SO] compliant annotations. The sequences will be available using the file format [http://www.sequenceontology.org/gff3.shtml GFF3].<br />
<br />
For discussion on standardizing URLs for accessing this information please see the GMOD wiki page <br />
[http://www.gmod.org/wiki/index.php/Standard_URL Standard URL]<br />
<br />
{| border="1"<br />
|+align="bottom" style="color:#e76700;"|''Where to find SO compliant GFF3 annotations for the Reference Genome sequences. ( * means that the presented file is not yet SO compliant)''<br />
|'''Organism'''<br />
|'''Organization'''<br />
|'''Download'''<br />
|'''Date'''<br />
|-<br />
|Drosophila melanogaster (Fruitfly)<br />
|[http://www.flybase.org FlyBase]<br />
|ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff <br />
|9/12/07<br />
|-<br />
|Caenorhabditis elegans (Worm)<br />
|[http://www.wormbase.org WormBase]<br />
|ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3<br />
|?<br />
|-<br />
|Saccharomyces cerevisiae (Budding yeast)<br />
|[http://www.yeastgenome.org SGD]<br />
|ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff<br />
|?<br />
|-<br />
|Dictyostelium (cellular slime mold)<br />
|[http://www.dictybase.org dictyBase]<br />
|http://www.dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=gff3&ID=dicty_gff3.zip<br />
|updated weekly<br />
|-<br />
|Arabidopsis thaliana<br />
|[http://www.arabidopsis.org/ TAIR]<br />
|ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR7_genome_release/TAIR7_gff3<br />
|8/15/07<br />
|-<br />
|Danio rerio (Zebrafish)<br />
|[http://zfin.org ZFIN] [http://www.sanger.ac.uk Sanger Institute]<br />
|Vega: ftp://ftp.sanger.ac.uk/pub/vega/danio/gff3/vega_danio_rerio_20070803.gff3 <br> Ensembl*: ftp://ftp.ensembl.org/pub/current_gtf/Danio_rerio.ZFISH7.47.gtf.gz<br />
|With new releases<br />
|-<br />
|Mouse<br />
|[http://www.informatics.jax.org/ MGI]<br />
|? <br />
|?<br />
|-<br />
|Human<br />
|[http://www.ebi.ac.uk/GOA/ GOA]<br />
| ftp://ftp.ensembl.org/pub/current_gtf/Homo_sapiens.NCBI36.47.gtf.gz<br />
|?<br />
|-<br />
|Schizosaccharomyces pombe (Fission yeast)<br />
|[http://www.sanger.ac.uk/Projects/S_pombe/ Sanger Centre]<br />
| * ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/<br />
|3/16/07<br />
|-<br />
|E.coli<br />
|[http://asap.ahabs.wisc.edi ASAP]<br />
|https://asap.ahabs.wisc.edu/asap/download_gff3.php?LocationID=&SequenceVersionID=&GenomeID=<br />
|?<br />
|-<br />
|Rat<br />
|[http://rgd.mcw.edu/ RGD]<br />
|ftp://ftp.ensembl.org/pub/current_gtf/Rattus_norvegicus.RGSC3.4.47.gtf.gz<br />
|?<br />
|-<br />
|}<br />
<br />
== Nota bene ==<br />
# The human and zebrafish Ensembl data is in GTF (not GFF3)<br />
# The pombe files are not (yet) valid GFF3. The known problems are:<br />
#* extra column 10 "Name"<br />
#* extra column 11 "orf_classification"<br />
#* extra column 12 "gene"<br />
#* extra column 13 "chr"<br />
#* the mandatory "phase" column isn't filled in.<br />
#* and the attributes" column may not be formatted correctly.<br />
<br />
Back to: [[Reference_Genome_Focus]]</div>Vpetrihttps://wiki.geneontology.org/index.php?title=GO_18th_Consortium_Meeting_Minutes_Day_1&diff=10111GO 18th Consortium Meeting Minutes Day 12007-10-24T17:21:14Z<p>Vpetri: /* Introductions chronologically: */</p>
<hr />
<div>Sunday morning, September 23, 2007<br />
([[GO 18th Consortium Meeting Minutes Day 2|Day 2 Minutes]])<br />
<br />
== Introductions chronologically: ==<br />
<br />
'''2007''' Dmitry Sitnikov MGI, Seth Carbon BBOP<br />
<br />
'''2006''' Jim Hu E. coli, Susan Tweedie FlyBase, Trudi Torto-Alalibo PAMGO, Donghui Li TAIR<br />
<br />
'''2005''' Ben Hitz SGD<br />
<br />
'''2004''' Doug Howe ZFIN, Ruth Lovering UCL<br />
<br />
'''2003''' Jen Deegan GO, Emily Dimmer GOA, Alex Diehl MGI, Mary Dolan MGI, Karen Eilbeck SO, Petra Fey dDB, Ranjana Kishore Caltech, Pascale Gaudet dDB, Victoria Petri RGD, Kimberley Van Auken Caltech<br />
<br />
'''2002''' John Day-Richter BBOP, Eurie Hong SGD, Tanya Berardini TAIR, Amelia Ireland GO<br />
<br />
'''2001''' Rama Balakrishnan SGD, Michelle Gwinn Giglio TIGR, Harold Drabkin MGI<br />
<br />
'''2000''' Rolf Apweiler EBI, Val Wood Sanger, Rex Chisholm dDB, Chris Mungall BBOP<br />
<br />
'''1999''' Midori Harris GO, Kara Dolinski PU, David Hill MGI<br />
<br />
'''1998''' Suzi Lewis BBOP, Michael Ashburner, Mike Cherry SGD, Judith Blake MGI<br />
<br />
== Progress Reports ==<br />
<br />
Next year the GO Consortium effort will celebrate its 10th birthday.<br />
<br />
2007 Progress Report for NHGRI due Jan. 1, 2008<br />
<br />
These reports will review accomplishments to date. <br />
We are using the itemized list of sub-aims from the grant to organize these <br />
<br />
Aim 1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.<br />
<br />
<br />
=== Ontology development ===<br />
<br />
== Ontology Development 1 - Midori Harris ==<br />
<br />
All content meeting related changes documented on [[Ontology_Development|Ontology Development Wiki]]<br />
<br />
is_a complete was almost finished last meeting, but is now done and a system is in place to make sure it remains so.<br />
<br />
:Three high level terms need to be disjoint – cellular process, multicellular organism process and multi-organism process. General notes on is_a complete: [[Isa-complete_BP]]<br />
<br />
Topics also overviewed; priority list on main Ontology Development wiki page.<br />
<br />
Content meetings have been held for:<br />
* [[Cardiovascular physiology/development|Cardiovascular Physiology]]<br />
* [[Muscle Development]]<br />
<br />
Other topics:<br />
* [[Transporters|Transporter activities]] extensive work via web conferences<br />
* Medium-scale content changes:<br />
** synaptic plasticity<br />
** [[RNA processing]]<br />
<br />
Michael Ashburner: Question IMG-to-GO and FIGS-to-GO mappings.<br />
<br />
:Jen, Midori: the IMG to GO mapping is mostly finished. These items are waiting for Jane to return.<br />
<br />
Chris M: mappings between the BP and MF terms still need to be done.<br />
<br />
JB/SL: wiki is a valuable resource, however it can get muddled sometimes – managers should keep track. <br />
<br />
Alex: if you add new large section you should send out a general email.<br />
<br />
'''ACTION ITEM – tutorial on wiki discipline (assigned to Jim Hu).''' <br />
<br />
Rex – in addition, there could be a group of wiki experts formed, who people could contact for advice.<br />
<br />
== Ontology Development 2 - David Hill ==<br />
<br />
=== 1) Taxon and sensu. ===<br />
<br />
“Sensu” confused users and curators, and editors became lazy in its implementation and accurate definitions were not created. Sensu terms have been renamed, merged or obsoleted (how many?) in collaboration with domain experts.<br />
<br />
:Note added after meeting: We would have to run obodiff to get counts for renamed vs. merged vs. obsolete, but we started in April with 229 'sensu' terms, and there are now 80 remaining in the live file. Of these, several are sorted out in the 'fruiting_body.obo' file in go/scratch/, and the remainder (about 60) are listed on the last [[Meeting_Notes_3|sensu meeting notes page]].<br />
<br />
Definitions now need to state how a process occurs differently in the different organisms. If it is impossible to state this, then child terms will not be created. In future, term requests need to include reasons how a process occurs differently in different organisms.<br />
<br />
Synonyms containing the sensu information are kept for these terms.<br />
<br />
The general consensus at the meeting seemed to be that rather than create long convoluted term names, we would still be allowed to create a term such as plant-type vasculature as long as the definition clearly differentiated the terms.<br />
<br />
==== Function-Process Links ====<br />
<br />
Chris M: these mappings are complex<br />
<br />
Waiting for OBO-Edit 2.0 for help on cross-products.<br />
<br />
=== 2) Regulation. ===<br />
<br />
[[Regulation Main Page]]<br />
<br />
GO will soon add a new relationship, 'regulates'. Regulation-of-process terms will then be changed from part_of the process to regulates (for example, 'regulation of metabolism part_of metabolism' will become 'regulation of metabolism regulates metabolism').<br />
<br />
During the is_a-complete work, three top-level regulation terms were added to represent three categories of biological regulation: regulation of molecular function, regulation of biological process, regulation of biological quality.<br />
<br />
Chris has generated a report (go/scratch/regulation-of-non-process.txt) of all descendants of 'regulation of biological process' where there is no term for the process being regulated. David Hill is going through the report (not as bad a task as he'd feared), and has found that the violations fall into three categories, corresponding to the three parts of the [[Regulation Worksheet]]:<br />
<br />
:[[Part 1]]: The regulation term describes regulation of a molecular function or a biological quality, so the term is o.k.<br />
<br />
:[[Part 2]]: The regulation term is a legitimate subtype of its parent, but a more specific process term isn't required. Example:<br />
<br />
::GO has 'regulation of transcription involved in forebrain patterning' and 'regulation of transcription', but not 'transcription involved in forebrain patterning'. 'Regulation of transcription involved in forebrain patterning' is<br />
<br />
::* Part_of forebrain patterning (check)<br />
::* Is_a regulation of transcription (check)<br />
::* 'Transcription of forebrain patterning' is not necessary -- it is essentially the same process as transcription<br />
This term will inherit the regulates relationship through its is_a paretn and will regulate 'transcription'. It will remain a part_of forebrain patterning since every instance of this process is a part_of an instance of forebrain patterning.<br />
<br />
:[[Part 1]]: Actual problems of various kinds; David has made suggestions about how to handle them, which everyone should check -- especially the ones with question marks.<br />
<br />
<br />
Chris Mungall: there are problems with cross-products, and would be easier if the parent terms did exist.<br />
<br />
David H: this will be resolved once the parent terms do exist.<br />
<br />
David H: concern about consistency in regulates relationships. In some cases, negative and positive regulation of a process are part_of the parent and in some cases they are is_a of the parent. We need to be consistent about this.<br />
For now, negative and positive regulation of a biological quality are a special case. When you are regulating a biological quality, the regulation is a balance of the positive and negative processes. Therefore, the positive and negative children are part_of the regulation of the quality.<br />
Suggestion to use homeostasis terms for overall regulation of biological quality [midori]<br />
<br />
CM: will look at relationships between cell types and GO terms: use as a guide to populate GO with missing terms.<br />
<br />
<br />
Q. VW: How existing annotations are affected by relationships change<br />
Eg transcription intiation. may have annotated more granularly to regulation of transcription initiation when there is direct involvement. Topic for annotation discussion at some point?<br />
<br />
A (David, Midori): The 'regulates' relationship shouldn't affect annotations. Basically the part_of relationships already exist and we will simply replace it with regulates. We are already annotating to regulates terms and it shouldn't change. What will be different is how we process annotations. We will be able to decide whether or not we should include regulates children.<br />
<br />
'''ACTION ITEM (ALL) Look at and comment on outstanding items (search on ?)''' <br />
<br />
'''ACTION ITEM Check whether there should be a relationship between pigment metabolic process and pigmentation'''<br />
<br />
=== 3) Information content analysis. Collaboration with MIT/Harvard group. ===<br />
<br />
MIT and Harvard got in contact with GO, were interested in measuring information content of a GO term.<br />
They looked at the number of annotations to a term related to its position in the ontology. <br />
<br />
They developed a statistical algorithm to determine information content based on the assumption that if not many genes are annotated to a term it has a high information content and a term with lots of gene products annotated has a low information content<br />
<br />
David, Midori and Jane then looked for outliers with respect to information content (finding terms that were either too specific, at a higher or lower level than they should be)<br />
<br />
Took higher level terms which had too few annotations compared to other things the same distance from the root and looked if they could be relocated. e.g pilus retraction was a direct child of 'cell physiological process' and was relocated to pilus organisation and biogenesis, so that it was at an appropriate level in the GO hierarchy.<br />
<br />
Similarly lots of specific terms had a larger than expected number of annotation eg. Olfactory receptor activity<br />
<br />
Some of the annotation distributions between terms also just reflected biological differences e.g. cation and anion transport terms: there are more cation transporter genes than anion transporters, the two terms are at the same level in the ontology - as they should be.<br />
Therefore this analysis can only draw attention to particular parts of the ontology which a curator then can examine.<br />
<br />
Q: JDR Is it possible to put this analysis into GOC tools? <br />
<br />
A: CM – the analysis is already in database, can be used.<br />
<br />
AD: this is something which can be repeated semi-regularly, but not to dwell on too much.<br />
<br />
DH: this has beeen a very good collaboration experience, and had produced good contacts to continue relationships with.<br />
SR: We know of other groups that could also get in touch which are interested in this area as well - will get in touch with David Hill.<br />
JB: annotations give power to these kinds of approaches. And until we have an annotation core we are restricting this kind of potential activity.<br />
<br />
== Ontology Development 3 - Chris Mungall ==<br />
<br />
Wiki for ontology structure (should be merged with Ontology Development)<br />
<br />
http://gocwiki.geneontology.org/index.php/Ontology_Structure<br />
<br />
<br />
1. Mining Reactome links to link process to function – more after lunch.<br />
<br />
<br />
2. Internal cross products can start to be created and maintained in the ontology. OBO-Edit 2.0 will make it easier to maintain these cross products. <br />
<br />
New cross product guide on wiki. Links to ongoing work on BP – CP cross products;<br />
<br />
e.g. could link histone deacetylase complex to histone deacetylase activity (this type of linking is easier than creating BF to MF links)<br />
<br />
<br />
http://gocwiki.geneontology.org/index.php/Cell_cross-products<br />
<br />
Includes:<br />
<br />
Internal links (existing)<br />
<br />
External links (function to process links)<br />
<br />
External links (x products)<br />
<br />
Links need to be treated with caution. Links are kept in a file separate to GO at the moment, as people could make erroneous propagation of annotaitons between the Gene Ontologies (i.e. just because someone annotates to a certain process, it does not mean they should necessarily annotate to the linked function).<br />
<br />
3. contributes_to<br />
<br />
- people are using this qualifier incorrectly in annoations.<br />
VW: take Histone Deacetylase complex as an example, this is a very large complex with many molecular functions. Therefore one complex can be linked to many different functions. We should use contributes_to *only* in those instances where the annotator does not know which subunit provides a function.<br />
JB: no, contributes_to can be used also when you *do* know the individual contributions of subunits.<br />
MD: often subunits which do not have a specific activity themselves are involved in enabling another subunit providing the activity.<br />
VW: but this does not hold ofr all complexes, we are using this qualifier in too many different ways.<br />
DH: often, if a subunit is knocked-out, the observer cannot tell if the subunit has a direct or indirect influence on the resulting phenotype. Therefore in addition often the 'contributes_to' qualifier is missing.<br />
: discussion postponed<br />
<br />
<br />
Internal cross-products<br />
If cross-products were maintained in the GO directly, it would make life easier. Cross-products will be more manageable in OBO-Edit 2.0 where there are many features - can use a 'Cross-Product Matrix Editor' - can see the possible cross-product/GO combinations, parents and children of a term.<br />
- this helps identify missing links in the DAG.<br />
- in addition, there will be an ontology repair option, which can introduce these links, e.g. missing is_a links.<br />
DH: we want to use this to go through the logic of the regulates relationship - as concern about ensuring consistency.<br />
CM: will also look at relationships bettween cell types and GO terms: and can use as a guide to populate GO with such missing terms.<br />
... more on cross-product logistics later.<br />
<br />
=== Karen Eilbeck SO Progress ===<br />
<br />
Development : March–>August joined J Thornton group - Gabi Reeves for BioSapiens project on protein terms, 96 new terms for polypeptides have now been added to SO. <br />
<br />
Mark Hathon (with Barry Smith)BioSmith, Buffalo – ongoing work on regulatory regions.<br />
<br />
Content meeting in June, HLA immunology community – looking for terms to describe variants. Added new terms, rearranging of SO – very productive.<br />
Assigned work to Alex, nothing to report. <br />
<br />
Collaboration with Arian at phyGo. Mobile genetic elements for viruses. This is in parallel with work happening in GO.<br />
<br />
Working on synonyms with Colin Batchelor, and over 400 new synonyms have been added to SO.<br />
<br />
Release SO now every 2 months. Therefore there is a stable and leading-edge version for those interested.<br />
<br />
Changing requirements for GFF3 - this not done yet.<br />
<br />
Karen dropping down to 60% on this project.<br />
<br />
<br />
'''COFFEE BREAK'''<br />
<br />
<br />
Aim2: We will comprehensively annotate reference genomes in as complete detail as possible.<br />
<br />
<br />
=== [[Reference Genome Annotation Project]] - Rex Chisholm ===<br />
<br />
Aim3: We will support annotation across all organisms.<br />
<br />
<br />
[[Image:ReferenceGenomes GOC PU 2007final.ppt]]<br />
<br />
Purpose: to provide comprehensive, robust collection of annotations for 12 genomes. <br />
These genomes have the most published data, have a genome database and experienced GO annotators. These high-quality annotations will be a resource for other groups to transfer to genes in their species.<br />
<br />
Complete/comprehensive annotation includes measures of breadth and depth. <br />
<br />
Breadth – every gene annotated. <br />
<br />
Depth – gene annotated to the highest possible knowledge. <br />
If there are only a small amount of papers (5-10) then the curator should read all. <br />
If extensive then the curator should be selective, completion best assessed by a curator)<br />
<br />
== Target Gene Identification (Priority genes) ==<br />
<br />
250 genes have now been targeted for curation. <br />
The target method has now been changed, targets are now (as of last month) selected based on disease type. Gene when mutated should contribute centrally to a disease phenotype(OMIM).<br />
This method has been generally successful, however there is now a challenge for mammalian groups with the increased literature load. Also a challenge for non-mammals - orthologs may not always be available (e.g. neurological genes in yeast). These challenges need to be balanced.<br />
<br />
== Ortholog Identification ==<br />
<br />
Need to have a good set of orthologs.<br />
<br />
Need to find ways of facilitating this work through tools, no obvious choice as yet. e.g. InParanoid have problems in keeping pace and providing up-to-date sets.<br />
Would be good to have a ortholog set automatically provided which curators could then validate.<br />
<br />
Software<br />
<br />
Currently use Google spreadsheets for target lists and information on curation progress.<br />
However this is not robust enough and time consuming. <br />
A database will be developed to handle this data and requirements have been written up. This will mean that the Ref Genome data is more structured. The database will provide a consistent use of identifiers, MOD association file loading, tracking when no ortholog found, and an automated response if a paper appears after a 'comprehensive date'.<br />
Sohel Merchant (left in July) wrote prototype<br />
<< ADD URL>>. <br />
A new member of staff will start at the end of September to continue development.<br />
<br />
<br />
== Metrics ==<br />
<br />
Annotation Progress – see slide.<br />
<br />
Annotation Consistency.<br />
<br />
<br />
Mary Dolan's tool for comparing annotations by looking at generic GOSlim branches useful as different organisms are used in different experimental approaches and different levels of data are available in different organisms.<br />
Eurie: if there is an outlier in annotation consistency checks this might also indicate organism-specific data (e.g. chromatin silencing not appropriate term for yeast).<br />
<br />
Table View (slim showing each terms annotated for a gene) includes every term useful for curation and annotation consistency (add link???).<br />
<br />
Ontology Development<br />
Aim to have robust discussions on annotation and ontoloo9gy development issues. Number of sourceforge requests from reference genome group in the hundreds over 16 months. There is an average of 10-12 SourceForge requests per month. GO editorial group doing a good job at keeping up with these. Existing requests are problematic. 411 terms.<br />
- It is important that curators label their SourceForge request as relating to a Reference Genome group.<br />
<br />
MH: Can retrieve number of GO terms that have resulted from these requests by looking at the cross-references file: 411 terms from Reference Genome-marked reqests.<br />
<br />
Ruth Lovering's Metrics Document v3: [[Image:HowToCaptureMetrics3.doc]]<br />
<br />
<br />
Publicising<br />
- need to start publicizing Reference Genome work.<br />
<br />
<br />
== Annotation Outreach – Jen Deegan ==<br />
<br />
Aim: to find new groups to join the GOC annotation effort, and keeping track of new groups annotating and writing documentation to help get groups started. <br />
<br />
see wiki: <br />
http://gocwiki.geneontology.org/index.php/Annotation_Outreach_group_reports<br />
<br />
[[Media:outreach_princeton.ppt]]<br />
<br />
Jen described the scope and techniques of outreach effort. Showed an 'ontology ' of outreach effort. There has been much progress on grants. <br />
<br />
Attending many regular conferences.<br />
<br />
Less cold calling, it wasn’t very successful. More luck tracking down the right person at conferences. Responding to invitations.<br />
<br />
<br />
People going to meeting – report back information from willing people to Jen.<br />
<br />
The SOPs have been tricky but are now on the public GOC website:<br />
<br />
http://www.geneontology.org/GO.annotation.SOP.shtml<br />
MA: this page is difficult to find.<br />
Action: this page needs to be reviewed and included in the next newsletter<br />
<br />
'''ACTION ITEM Jen: A reference to these pages should go in next newsletter.'''<br />
<br />
'''ACTION ITEM Jen Add a link from outreach to the SOPs)'''<br />
<br />
There has been funding success - for the British Heart Foundation and AgBase grants. <br />
<br />
MA: for new groups annotating, how many SourceForge requests are we getting? e.g. Aspergillus group should have requested new terms?<br><br />
SL: agree. As soon as an annotation effort really has started, the group often needs a number of new terms.<br><br />
<br />
Jen: for emerging genomes the main problem is finding funding to support an annotation effort.<br><br />
MC: need to determine if they are only doing IEA annotation, or whether they have the time to carry out manual curation.<br><br />
JH: the process of making new term requests is not obvious<br><br />
JW: the SourceForge term tracker only goes to the GO list, so other groups not aware<br><br />
MH: it is possible to add more e-mail addresses to this list.<br><br />
MA: not our job to source funding for new groups, it is the job of the individual groups. <br><br />
JB: supporting new groups is important, need to mentor groups and support them submitting new terms.<br />
<br />
'''ACTION ITEM investigate why terms requests aren’t coming in, do we need to do things to make it easier, SF tracker list/annotation list/ who are on these lists/ do other people need to be on those lists?'''<br />
<br />
<br />
<br />
== User Advocacy - Eurie ==<br />
<br />
Focusing on lines of communication, web presence, newsletter and mailing list. <br />
<br />
Different users, new users, current users, power users<br />
<br />
Most of the past year has focused on the lines of communication.<br />
<br />
wiki User Advocacy main page: <br />
http://gocwiki.geneontology.org/index.php/User_Advocacy<br />
<br />
Rota of mailing list monitors.<br />
<br />
Newsletters archived. Future news items page on wiki. <br />
Wiki or Newsletter ideas <<add link>><br />
<br />
Michael A wants ISSN for the newsletter. <br />
<br />
'''ACTION ITEM NML Michael sent URL to Eurie – Action Eurie!'''<br />
<br />
'''Somebody mentioned RSS feed, is this a potential action?'''<br />
<br />
Users meetings, we have a page of potential meetings on wiki.<br />
- used to target groups new to GO and help education.<br />
- have a workshop specific for microarray users (rather than an add-on to MGED)<br />
<br />
Tools standards. (Needs to be cleaned up and categorised)<br />
- ideas for minimum standards for GO tools<br />
- send out list a month ago:<br />
http://gocwiki.geneontology.org/index.php/Tools_standards<br />
<br />
== Production Systems - Ben Hitz ==<br />
<br />
[[Image:ProductionReport_GOC_PU_2007.ppt]]<br />
<br />
Deployed 4 new linux machines 1 for loading, 2 for AmiGO production, 1 AmiGO development.<br />
<br />
Production AmiGO now more fault resistant.<br />
ACTION: e-mail Ben if you are not getting a gp2protein check for your database.<br />
<br />
Go Database loading speeded up and now in testing.<br />
<br />
Godb sequences – using gp2protein files. If possible do all sequences in your DB, not just annotated.<br />
<br />
Assocdb fasta file – Header line massive – can be slimmed down?<br />
<br />
Association file cleaning – All IEAs must have a with field.<br />
<br />
== AmiGO – Amelia ==<br />
<br />
AmiGO enhancements and new search features demo<br />
<br />
*Search result relevance implemented - most 'relevant' results are shown first<br />
*Term and gene product search is now "intelligent" and AmiGO will automatically search all fields if it doesn't find a match.<br />
*Term enrichment (also known as "GO Term Finder") and GO Slimmer (map2slim) functionality have been added to AmiGO. Both can use uploaded user files or data from the GO database.<br />
*Downloads in OBO, RDF-XML and gene association format now possible<br />
<br />
'''LUNCH BREAK'''<br />
<br />
== Action Items Review ==<br />
<br />
This large section moved to it's own page:<br />
<br />
[[Outstanding Action Items from 17th GOC Meeting, Cambridge UK]]<br />
<br />
Afternoon, Sunday, Sept 23, 2007<br />
<br />
== Reactome - Peter D’Eustachio ==<br />
<br />
[[Image:Reactome_to_GO_GOC_PU_2007.ppt]]<br />
<br />
Reactome can provide data to proteins that UniProt does not yet have manual annotations for most of this Reactome data is derived from experimental evidence identified from papers however unlike the GO annotation method, the types of experiments have not been recorded.<br />
<br />
Emily: GOA would love this data, but unless have a new parent ‘Experimental’ code, the best that exists is ‘TAS’.<br />
<br />
Suzi Lewis: there is a use for a hierarchy of evidence codes. With an ‘E’ Experimental code as a parent of the IMP, IGI, IDA, IPI, IEP granular codes.<br />
<br />
Peter: Homolog sets used to transfer data between species is determined by individual experts, and transfer between orthologs AND homologs (where functionally similar)<br />
<br />
Judy and Suzi: Reactome data is valuable. It is unacceptable to not be including it in GO and it is unacceptable that this data should have anything less than an experimental evidence code. TAS or NAS evidenced data are unacceptable also.<br />
<br />
Peter: current Reactome curation methods is to avoid unpublished data and Reactome curators also want to be opinionated about the published data, to the end that Reactome will reflect current expert opinion, and avoiding hypothetical theories. Only confirmed, accepted knowledge is included. There are 10 curators, only 2 of whom have previous experience in GO annotation, there is no budget to do GO annotation and no desire to teach curators about GO evidence codes. Don’t always know which piece of literature applies to which info.<br />
2000 gene annotated. 4000 pieces of literature. It is not clear how many GO annotations this would convert to.<br />
<br />
Suzi Lewis: This brings up the question of what is the purpose of evidence codes? Why do we have the ones we have? Do users use them? (something to discuss tomorrow). <br />
<br />
Pascale: have evidence from users that they do care whether IDA or IMP codes are used.<br />
<br />
Peter: There is not always a 1 GO term to 1 publication relationship. Sometimes a GO term may have originated from the combined curation of many papers.<br />
<br />
Eurie and John Day-Richter: TAS annotations are valuable, and may be good to get the data in.<br />
<br />
Suzi, Judy: this data is too good for TAS.<br />
<br />
Emily D: Why not use a mix of codes depending on the GO term to publication ratio? For those instances where there is a 1:1 relationship of GO term to publication: use ‘E’, for 1 GO term to many publications: use ‘TAS’ and cite the Reactome reaction web page as the source – this then acts as the reviewed document.<br />
<br />
David Hill: concerned about the proposition of a new ‘Experimental’ evidence code: might loose analytic power.<br />
<br />
Judy B: could Reactome curators go back and re-annotate those 4,000 papers and convert the codes to one of the GO experimental codes? This would only take 2 weeks to do.<br />
<br />
Peter: Not possible – Reactome have defined goals, we cannot afford to reannotate for GO. 75 genes/month is the absolute minimum annotations. We have our own grant objectives we must fulfill. <br />
<br />
David Hill: GO curators could prioritize the reannotation of genes for which there is not much annotation available.<br />
<br />
Rex: could the reference genome groups each take on a subset of annotations and re-annotate?<br />
<br />
Emily: then the annotation would belong to the group that reannotated. We would be using Reactome data as a source, but the final annotations would be attributed to the group that provided the final annotations. Might not be the best use of resources.<br />
<br />
Suzi : Would accept ‘EXP’ for the 1:1 mapping of GO term to publication. <br />
<br />
<br />
Q Val: Any idea how many aren’t covered by GO annotation already? <br />
A. No…<br />
<br />
<br />
Judy, Sue R, Emily D, Tanya B: the ‘EXP’ code would make life easier for users, for other integrations as well<br />
<br />
'''ACTION: Reactome annotations should be available from GO by the next GO Consortium meeting. Chris, Alex, Jen and Ruth to be responsible. Add new evidence code EXP for 1:1 Reactome to literature, add all other Reactome with TAS to Reactome source.'''<br />
<br />
Arguments for structuring evidence codes<br />
i) make things simpler<br />
ii) allow incorporation of other date<br />
iii) needn't change our current usage<br />
iv) do the TAS for the things that don’t fall under EE that can’t be assigned to a single paper.<br />
<br />
(continue tomorrow the discussions of the point of evidence codes and the possibility of new parent ‘EXP’ code)<br />
<br />
<br />
=== Protein Complexes: GO vs/ Reactome ===<br />
<br />
Reactome complexes are seen as an entity, (i.e. a collection ofo proteins) whereas GO treats complexes as a subcellular location<br />
However there is also a blurring between the two for Reactome, especially when looking at large complexes.<br />
Peter: In our annotations, a cross-reference slot allows us to cite a GO identifier for the location (usually to the parent term of the complex). Reactome curators add the cc term that is most granular, and willing to generate SourceForge request for those missing<br />
<br />
Judy B: talked to Lisa in Bar Harbor on complexes for Reactome. Concern about the active function tag to the active polypeptide. <br />
<br />
Peter: for a catalysis – any physical entity in a complex is given a GO term describing the activity, however the active unit, which mediates the reaction is labeled by Reactome. Can parse out which of the polypeptides had the catalysis functions and which are just associated – in most cases this is identified by experimental data.<br />
Although Reactome does not always search for the most granular Biological Process GO term, these haven’t been applied consistently.<br />
<br />
David Hill: there should be no problem mapping this data from Reactome, while the concepts in GO and Reactome are not equivalents this is not a problem as GO would annotate the same gene products as Reactome would.<br />
<br />
Peter: Ewan did have a concern about the ‘contributes_to’ qualifier – concerned that a significant number of end users would not always be aware of use contributes_to. But really this is the users problem. And they can strip out if necessary.<br />
<br />
Jennifer: users have suggested that GO could strip out annotations which use the contributes_to column (especially the NOT annotations) and these then could be provided as a separate file. As these can be dangerous to ignore.<br />
<br />
<br />
'''ACTION ITEM convert Reactome complex terms to GO terms'''<br />
<br />
== ‘Taxon and GO’ - Jen Deegan ==<br />
<br />
[[Image:Taxon_and_GO_GOC_PU_2007.ppt]] (using paper from Waclaw Kusnierczyk)<br />
<br />
Originally Chris and Jen worked to loose sensu tags and redefining definitions and adding taxon links <br />
- However removal of taxon has been a problem. There are now 23,802 terms. Searching for terms is a time sink for users, <br />
- GO help has often received queries from users asking if there is a taxon-specific GO slim/subset of terms (e.g. plant-specific GO)<br />
<br />
- In addition, Jen as outreach officer has found new MOD groups are unwilling to annotate to GO unless there is a slim available for them.<br />
<br />
- GO language can be subtle. GO term names can now be complex now the sensu information has been removed. This would make GO terms easier to find and decipher.<br />
<br />
- In addition, having taxon information in the GO helps error checking <br />
<br />
- There are 3 types of relationships that could be applied to relate taxon to GO terms:<br />
1. Is_relevant_to<br />
` 2. is_only_in<br />
2. applies_to_all<br />
<br />
This taxon-specific information would be added into a separate file.<br />
<br />
Discussion:<br />
<br />
Judy: Against including taxon information within the GO as we do not know all properties of a taxon. Taxonomic information is in flux also, we do not want a dependence on taxonomy in GO. We would be restricting ourselves if we did not make all terms available to all users.<br />
Could not instead users look at the terms that were used by a reference genome group to see what terms are appropriate for a particular taxon?<br />
<br />
- general disagreement from curators of this possibility.<br />
<br />
Agreement that there are incorrect annotations which relate to taxon-specific properties:<br />
Harold: in the Phantom load – needed to remove incorrect mouse annotations<br />
<br />
Val, Harold: InterPro2GO throw out problems. These could be identified by this method.<br />
<br />
Val: I perform monthly checks to ensure no inappropriate terms have come in at high level. This is time consuming, and this would help.<br />
<br />
Pascale: would help sanity check annotation data<br />
<br />
Val: this species information doesn’t need to be comprehensive to be useful for annotation checks<br />
<br />
Eurie: if this would help annotators, this information could be built into an annotation tool?<br />
<br />
Ruth: there are interesting concepts here, but does it need to be so complicated, would all taxons need to be included. Could we not instead just use just 10 high-level taxon identifiers.<br />
<br />
Judy: Instead, could not rulebase triggers be used Efforts should be on annotation of literature rather than waste a considerable amount of time incorporating taxon information. We do not want to commit such a level resources to such a project especially as budgets are stretched presently. Again, concern about fluidity of taxon-specific information<br />
<br />
Sue Rhee: we should explore usage of GO slims.<br />
<br />
Suzi Lewis: there are risks in this kind of project, and concerned that this project would entail quite a bit of work and could also be misunderstanding by users. Can we have a low-key evaluation.<br />
<br />
JDR: a large-scale activity of this – is a bad idea. You would propagate garbage by accepting all annotations. Could use as just a framework by only using 10 top taxon id. – this would already help find problems.<br />
JC – agreed.<br />
<br />
Alex D: Isn’t this just a user education problem? Users need to take the time to understand the GO hierarchy, that you can search synonyms, definitions etc. Feel that user queries are symptoms of users not trying hard enough to work with GO.<br />
<br />
Mike Cherry: could not afford to make this a big project, there are other developments in GO which need to be addressed <br />
<br />
Rex: Had concern about making taxon-specific assertions that are flawed.<br />
If these types of sanity checks or limits were automatically applied, we would loose the potential value of not looking into these, however this data would probably tell us something fundamental about biology, and loose the ability to investigate these.<br />
<br />
Judy: classifications of taxon are based on phenotypes and not molecular data and many things are being found and taxons are being redefined. Prefers’ is_relevant_to’<br />
Like the idea of flags/triggers to factiliate work, but wouldn’t automatically exlude, as this data is important.<br />
<br />
Michael A: while some taxonomy is changing e.g. in protista, it is unlikely that viridplantea or mammalian will move around so much.<br />
<br />
Ben Hitz: what fraction of problems would be solved if there were cross-products to taxonomy were included?<br />
<br />
Jen Deegan: it would solve some, it would help with the development terms.<br />
<br />
Ben Hitz: what would the time line be for taxon cross-products?<br />
<br />
Chris Mungall: this is much further down the line. <br />
<br />
Judy. Our main issue here is how to facilitate annotations in our groups. However but we are hung up on a suggestion from outside the group. <br />
<br />
Chris Mungall: slims are much harder to maintain than these relationships would be.<br />
<br />
Michelle M: When the prokaryotic subset was created, she was v much against. Instead of users looking at 20,000 terms, they are now looking at 9,000 – there is not that much benefit. Don’t think new users need this, need to facilitate better ways of finding terms within the tool. For curators it might be useful for error checking, but not new users.<br />
<br />
JDR: although there is a big concern that you’d loose annotations because of these relationships, this would not be the case as the incorrect annotations would instead be brought to your attention – and visible to better investigate/ or improve GO. the rules could be fixed.<br />
<br />
<br />
Ruth: how would this data be viewed ? In addition, if a user does not understand a term then it really is a problem with the terms definition – instead the definition needs to be improved, this would be far more valuable than adding in an additional cross-link.<br />
<br />
Jen: will be willing to carry out a small pilot version of this task in her own time. Would add 10 is_only _in relationships and use these and the annotations<br />
to check for errors in the annotations and the ontology structure. <br />
<br />
'''ACTION: Jen to do a pilot project with a minimal set of terms, as an experiment and bring back results for next GO meeting'''<br />
<br />
'''ACTION: (David Hill) Make difficult sensu terms organism specific (biologist intuitive) (i.e plant vacuole, fungal vacuole). However GO definitions will still be designed to be formal, not depending on species to define the term.<br />
'''<br />
<br />
== Summary of action Items from Day 1 ==<br />
<br />
# Tutorial on wiki discipline (assigned to Jim Hu ?).<br />
# (ALL) Look at and comment on outstanding items [[Outstanding Action Items from 17th GOC Meeting, Cambridge UK]]<br />
# Check whether there should be a relationship between pigment metabolic process and pigmentation <br />
# Jen: A reference to these pages should go in next newsletter.<br />
# Jen Add a link from outreach to something (SOP?)<br />
# investigate why terms requests aren’t coming in, do we need things we need to do to make it easier, SF tracker list/annotation list/ who are on these lists/ do other people need to be on those lists? <br />
# NML Michael sent ISSN URL to Eurie – Action Eurie!<br />
# e-mail Ben if you are not getting a gp2protein check for your database.<br />
# Somebody mentioned RSS feed, is this a potential action?<br />
# Reactome annotations should be available from GO by the next GO Consortium meeting. Chris, Alex, Jen and Ruth to be responsible. # Add new evidence code EXP for 1:1 Reactome to literature, add all other Reactome with TAS to Reactome source.<br />
# Convert Reactome complex terms to GO terms<br />
# Jen to do a pilot project with a minimal set of terms, as an experiment and bring back results for next GO meeting<br />
# (David Hill) Make difficult sensu terms organism specific (biologist intuitive) (i.e plant vacuole, fungal vacuole). However GO definitions will still be designed to be formal, not depending on species to define the term.</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Individual_MOD_Reports&diff=9885Individual MOD Reports2007-09-21T18:08:21Z<p>Vpetri: </p>
<hr />
<div><!-- Please insert a hard return after the last item, dd your DB tittle and a link to your file (uploaded to the Wiki)--><br />
MGI:<br />
http://link to mgi report<br />
<br />
SGD<br />
http://link to SGD report<br />
<br />
ZFIN<br />
http://gocwiki.geneontology.org/images/0/07/ZFINprogress_2007v2.doc<br />
<br />
GO Editorial Office<br />
http://gocwiki.geneontology.org/images/8/83/GO_Ed_report_2007-prelim.doc<br />
<br />
WormBase<br />
http://gocwiki.geneontology.org/index.php/Image:WormBase_GO_Report_Princeton07.doc<br />
<br />
TAIR<br />
http://gocwiki.geneontology.org/index.php/Image:TAIRProgressReport_Sept2007.doc<br />
<br />
RGD<br />
http://gocwiki.geneontology.org/index.php/Image:MODProgressReportTemplate_2007_RGD.doc</div>Vpetrihttps://wiki.geneontology.org/index.php?title=File:MODProgressReportTemplate_2007_RGD.doc&diff=9950File:MODProgressReportTemplate 2007 RGD.doc2007-09-21T17:46:20Z<p>Vpetri: Preliminary Progress Report from RGD</p>
<hr />
<div>Preliminary Progress Report from RGD</div>Vpetrihttps://wiki.geneontology.org/index.php?title=Orthology_discussion_page_(Retired)&diff=7662Orthology discussion page (Retired)2007-05-14T15:47:05Z<p>Vpetri: </p>
<hr />
<div>This is the place for general discussions of methods, problems or ideas regarding general principles for establishing orthology between reference genome genes and the human disease gene targets. <br />
<br />
Specific discussion of gene specific issues should be directed toward the gene specific pages. A link will be added here as soon as the pages are established.<br />
<br />
----<br />
<br />
== ZFIN Orthology Determination Method ==<br />
We always use the same methods as outlined here:<br />
<br />
1. Check to see if orthology has already been established between a<br />
zebrafish gene and the human gene by searching in ZFIN.<br />
<br />
2. If there is no established zebrafish ortholog, the human sequence is<br />
used to search zebrafish mRNA, Vega and Ensembl transcripts and protein<br />
sequences for potential orthologs. If there are several zebrafish sequences<br />
that are candidates for being the ortholog, reciprocal blasts of the<br />
zebrafish sequences against human sequences are used to order them. The best<br />
matches are then analyzed for conserved synteny with the human gene.<br />
<br />
The current version of the zebrafish assembly at Ensembl is used to<br />
determine the location of the zebrafish gene. After the zebrafish gene has<br />
been localized, the flanking regions around the gene are analyzed for other<br />
orthologous genes between zebrafish and human chromosomes. The presence of<br />
conserved synteny is used as evidence to confirm orthology and the human<br />
gene is assigned as the ortholog of the zebrafish gene in ZFIN. If<br />
necessary, the zebrafish gene nomenclature in ZFIN is updated.<br />
<br />
In cases, where sequence analyses and synteny do not provide clear evidence<br />
to distinguish between two or more zebrafish genes, orthology is not<br />
established. This is also the case for human genes that do not match any<br />
zebrafish cDNA or EST sequences but have a sequence match in the zebrafish<br />
genome. Genscan or FGENESH identifiers are instead provided as identfiers for<br />
putative zebrafish orthologs.<br />
<br />
== TAIR Orthology Determination Method ==<br />
<br />
We use YOGY and maintain a separate spreadsheet of results for each method (analysis not done included) for each human gene.<br />
If an Arabidopsis gene appears in more than one analysis, we consider it an Arabidopsis ortholog. Arabidopsis genes that only occur in one analysis are not considered orthologs.<br />
<br />
== dictyBase Orthology Determination Method ==<br />
<br />
1. Check YOGY for orthologs (if human name(s) are not recognized in YOGY search HGNC, UniProt or even Google).<br />
<br />
2. If there is an ortholog in YOGY (Dicty is included in two methods: Inparanoid and OrthoMLC) we confirm ortology with reciprocal BLAST. We have the rule that an ortholog should be at least 30% identical over 80% of the length of the protein; however, the curator can decide a protein with lower sequence similarity is an ortholog if there are single genes in both organisms. <br />
<br />
We also routinely compare domains in InterPro, including and/or Pfam, TMHMM and SignalP if the human protein contains such structures. This helps to firmly determine if there is a single Dicty ortholog.<br />
<br />
3. In case there is no ortholog in YOGY, we blast the human protein sequence in dictyBase and change parameters like E-value and/or turning filtering off if necessary (e.g. for very short proteins such as DNAJC19). If we identify a potential ortholog this way, we proceed with our analysis as described in 2.<br />
<br />
4. If Dicty has one or more genes that are just similar, e.g. conservation is only over a large domain, we do not consider this an ortholog. Depending on the degree of similarity we might mention this in our free-text description on each gene page.<br />
<br />
== SGD "Orthology" Determination Method ==<br />
<br />
# Check each human gene name in YOGY for hits with each of the four methods: KOG, Inparanoid, HomoloGene, and OrthoMCL. Record which ''S. cerevisiae'' genes come up as hits for the human gene via each method.<br />
# Evaluate whether I am getting the same hits from each of the available methods. Note that sometimes a given method is not available for a given human gene. In these cases, the comparison is made only between the results from the available methods.<br />
# Take the ''S. cerevisiae'' hits obtained by searching with the human genes and use YOGY to search for their orthologs. <br />
# Make a decision of what, if anything, to call, based on how many methods produced the ''S. cerevisiae'' hits, and on how many of the methods returned the original human gene as a hit in the reverse search with the ''S. cerevisiae'' gene. The examples below may help illustrate the decision process. <br />
<br />
'''Some Examples'''<br />
* '''Of getting hits but not making a call'''<br />
*# Sometimes I get hits in KOG, usually multiple hits, but no hits with any of the other 3 methods, where at least some of them were available. In cases like this, I take a look at the KOG info. When this occurs, the KOG usually turns to be something rather general, e.g. "permease of the major facilitator superfamily" as was the case for SLC37A4 (G6PT1; Glycogen storage disease Ib, 232220 (3)) and I ignore the ''S. cerevisiae'' hits coming from the KOG.<br />
*# For the human gene DPAGT2 [Congenital disorder of glycosylation, type Ij, 608093 (3)], Inparanoid and OrthoMCL give ScALG7 as a hit, though HomoloGene does not. However, searches with ALG7 give DPAGT1 rather than DPAGT2 so I did not make a call. <br />
* '''Of making a call'''<br />
*# Sometimes I get hits with some methods, but not others. For example, for DPM1 [Congenital disorder of glycosylation, type Ie, 608799 (3)], 3 methods (KOG, Inparanoid, and OrthoMCL) produced the same hit, ScDPM1, but HomoloGene, while available did not. When ScDPM1 was used to search YOGY, it produced the original human gene, HsDPM1, as the sole human hit by KOG, Inparanoid, and OrthoMCL. HomoloGene produced hits, but only in Kluyveromyces lactis and Eremothecium gossypii, both of which are also fungi. As I have sometimes seen this pattern before, where HomoloGene has a much narrower range of calls than both Inparanoid and OrthoMCL, I went with the consensus of the other methods and called ScDPM1.<br />
*# Sometimes I get the same hit with all four methods. For example, for the human gene G6PD [Favism (3)], all four methods produce the same hit, the ''S. cerevisiae'' gene ZWF1. Doing the reverse search with ScZWF1, all four methods produced HsG6PD as a hit, though two methods also produced two additional hits. In this case, I ignored the additional hits and called ScZWF1 as the best hit for HsG6PD.<br />
* '''Of a mistaken call'''<br />
*# For the human gene DPYD [Thymine-uraciluria (3)], Inparanoid and OrthoMCL hit URA1, KOG and HomoloGene while available for this gene did not call ScURA1. Search YOGY with ScURA1 gives back the original human gene with KOG, Inparanoid, and OrthoMCL. Thus I made the call. However, Julie Park, an SGD curator who had previously curated the ScURA1 gene in detail informed me that URA1 has a different specific human homolog, thus that ScURA1 is not orthologous to this human gene. The appropriate Human homolog for URA1 corresponds to GenBank ID: M94065 and is described in a paper (PMID:1446837) and an OMIM record (http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=126064). Julie added that there is a similar domain between the human DPYD gene (encoding Dihydropyrimidine dehydrogenase [NADP+]) and ScURA1 (encoding dihydroorotate dehydrogenase), but the similarity does not extend to the entire protein. So, while the called looked good in terms of the hits and reciprocal hits, it was actually false.<br />
* '''Of a case where I'm not sure whether I should have made a call'''<br />
*# For the human gene ACTC [Cardiomyopathy, familial hypertrophic, 192600 (3)], I got hits with 3 methods. For KOG, this was "Actin and related proteins" so it's not really specific enough to use. For both Inparanoid and OrthoMCL, I only got one hit in ''S. cerevisiae'', but the human gene 'ACTC1' pulled up multiple hits in human. For the Reverse checks: searching with Sc ACT1 (S000001855, YFL039c), I got the same general KOG and ignored it. Both Inparanoid and OrthoMCL pulled up multiple human genes, the starting human gene as well as many of the same human genes pulled up in the original search with HsACTC1. However, HomoloGene pulled up only HsACTG1, and not HsACTC1. I opted not to call this, but remain uncertain as to whether I should have or not.<br />
<br />
'''Further Comments'''<br />
# I would like to know more about the methodology behind each of the four prediction methods.<br />
# I would like to be able to see alignments of the results, or at least some indication as to whether the hit is across the full length or just to a domain.<br />
# In reverse searches with the ''S. cerevisiae'' genes, it is sometimes very difficult to determine whether the KOG hits actually correspond to the human gene I started with.<br />
# It's really time consuming to do the equivalent searches via the individual pages for KOG, Inparanoid, HomoloGene, and OrthoMCL. They all search differently. Some don't allow searching by the gene name and you have to use an ID, and not just any ID only the one they've chosen to reference.<br />
# Should we be using the word '''ortholog'''? Some people use a very precise meaning of ortholog. Do we really mean that here?<br />
<br />
From http://www.reference.com/browse/wiki/Homology_(biology):<br />
<br />
Orthologs, or orthologous genes, are any genes in different species, that are similar to each other and originated from a common ancestor, regardless of their functions. Thus orthologs are separated by an evolutionary speciation event: if a gene exists in a species, and that species diverges into two species, then the divergent copies of this gene in the resulting species are orthologous. The term "ortholog" was coined in 1970.<br />
<br />
A second definition of orthologous has arisen to describe any genes with very similar functions in different species. This differs from the original definition in that there is no statement about evolutionary relation, or similarity in sequence or structure.<br />
<br />
<br />
== WormBase: C. elegans Orthology Determination Method ==<br />
<br />
1. Check YOGY using the human gene name and record the number of hits from each method in the elegans spreadsheet, Column T. C. elegans gene products are included in all four methods, but if a method lists no elegans gene product, then that method is not included in Column T.<br />
<br />
2. If one C. elegans gene product is listed for each method, then that gene is entered as the ortholog of the human gene. We also perform reciprocal BLAST searches between the human and elegans proteins to confirm the orthology. BLAST scores are now being recorded in the spreadsheet.<br />
<br />
3. If there is no ortholog listed in YOGY, we still perform reciprocal BLAST searches and examine the highest scoring pairs. In some cases, for example ATXN2, this identifies an elegans ortholog that was not identified by the methods listed in YOGY.<br />
<br />
4. Since in some cases the C. elegans ortholog is highly diverged in sequence from the human protein (see BRCA2/BRC-2, for example), we also search WormBase and the C. elegans literature using Textpresso to see if there are identified orthologs whose sequence identity was not high enough to be returned in a BLAST search. (p53 and CEP-1 are another example)<br />
<br />
5. The trickiest cases are those for which there are a number of C. elegans protein that are identified in YOGY (usually via KOG analyses) and that are roughly equivalent matches as far as BLAST scores are concerned. This has happened, for example, with some transmembrane receptors and Forkhead transcription factors. In these cases, it's not always clear that there is a true elegans ortholog. However, since many of these genes play important roles in C. elegans development and/or behavior, there would no doubt be value in having them annotated in GO. We would like to annotate these genes as time permits, but may not include them as orthologs in our spreadsheet. <br />
<br />
6. We also examine the results of TreeFam analysis as listed on the gene summary pages of WormBase to corroborate the YOGY and BLAST results.<br />
<br />
<br />
== MGI: Mouse Orthology Determination Method ==<br />
<br />
1. MGI has, for a long time ( > 15 years), curated and maintained <br />
>orthology records for a variety of mammalian gene sets with a primary <br />
>focus on mouse/human/rat sets. Recently, we updated our full orthology set loads to include chimp and dog as a result of the sequencing of chimp and dog genomes. We will continue to add full ortholog sets as additional genomes are completed. We expect to extend our orthology sets to include other vertebrates in addition to mammals in the future (chicken for example).<br />
<br />
2. We now rely heavily on the sets resulting from Homologene algorithm. Homologene algorithms are re-run whenever there is a new <br />
genome release. We re-load Homologene sets following each new run. We <br />
are now loading orthology sets for mouse/human/rat/chimp/dog. We <br />
co-curate mouse data with EntrezGene curators for gene and sequence <br />
identities and intersections, orthology, etc. EntrezGene incorporates <br />
GO annotations from MGI. The EntrezGene files provides OMIM IDs for <br />
human genes as available.<br />
<br />
Homologene releases new data several times a year. But we only expect to see a major changes after a new genome build. So our updates are timed around a new genome build and/or a couple of times a year.<br />
<br />
3. We incorporate specific subsets of orthology assertions from <br />
Homologene. We also load addition orthologs where there is no conflict with existing orthology data. We obtain ~17,000 human/mouse ortholog <br />
determinations from this process, somewhat fewer numbers of rat/dog/chimp orthologs are included.<br />
<br />
Homologene compares the protein sequences and determines if a given gene has orthologs and annotate the data as one of the following.<br />
<br />
# Reciprocal best hits between two organisms (b)<br />
# Reciprocal best hits between more than 3 organisms (B)<br />
# A match between two organisms, not a reciprocal best (m)<br />
<br />
We take the b and B sets. Then we compare with our existing MGI data. The orthology sets that exactly match existing MGI data and any new Homolegenes sets that do not conflict with existing MGI orthology data are loaded as part of Homologne load. We follow the same steps for mosue-human, mouse-rat, mouse-chimp and mouse-dog data. We use a specific citation number to distinguish Homologene load. <br />
<br />
4. We supplement Homology orthology with additional orthology <br />
determinations from the HCOP set from HGNC. The HCOP project curates <br />
the Homologene, Compara, and Inparanoid ortholog set intersections to <br />
provide a unique representation of orthologs in humans and other <br />
mammalian species. Through this mechanism, we resolve some clusters <br />
that were filtered into QC reports from the Homologene load. From this <br />
process we obtain an additional 700+ ortholog sets.<br />
<br />
5. MGI orthology sets are available on our ftp site. Start here to see file structure. ftp://ftp.informatics.jax.org/pub/reports/index.html <br />
Then you can select the file of interest. If you need help or want some other file<br />
structure, contact MGI user support at mgi-help@informatics.jax.org<br />
<br />
== FlyBase Orthology Determination Method ==<br />
<br />
FlyBase use InParanoid for both reference genome and general FlyBase orthology calls. <br />
<br />
In detail:<br />
<br />
1. Search the HGNC site to find official human gene symbol and corresponding Ensembl gene ID.<br />
<br />
2. Search InParanoid with Ensembl gene ID for Drosophila melanogaster orthologs using the default parameters (exclude inparalogs scoring below 0.05).<br />
<br />
3. If result is 'no cluster' then report there is no ortholog.<br />
<br />
4. If the human sequence clusters with Drosophila sequences then report the Drosophila gene only if it is the 'main ortholog' of the human gene. This is in line with what FlyBase reports as orthology calls but is possibly too conservative.<br />
<br />
For instance, by our criteria there is 'no ortholog' for ACHE (acetylcholinesterase) based on the following InParanoid results:<br />
<pre><br />
Protein ID Score Bootstrap Gene<br />
ENSP00000264381 1 99% BCHE (human)<br />
ENSP00000350037 0.246 ACHE (human)<br />
FBgn0000024 1 99% Ace (fly)<br />
</pre><br />
BCHE is the 'main ortholog' of Ace but ACHE is also considered to be orthologous by InParanoid. There is clearly an argument for curating the Drosophila Ace gene even though it is more closely related to BCHE than ACHE. The decision to stick with curating 'main orthologs' is partly an attempt to be consistent (I started doing it this way) and also influenced by time limitations - I'm currently failing to keep up-to-date with curating even the 'main orthologs'. Also, if one fly gene is reported as the ortholog of many human genes we will end up with the same data in several rows of the spread sheet and end up with a inaccurately high impression of how much curation has been done in the metrics - is this a problem?<br />
<br />
5. Record either 'main ortholog', 'no cluster' or the most similar human/Drosophila gene pair from the cluster (e.g. BCHE/Ace in ACHE search) along with the search date in a local results spread sheet.<br />
<br />
Comments: At present if no cluster is reported by InParanoid, no further searches are performed. However, following the discussion of different methods, I have spot-checked a few genes using different methods and have not found any additional orthologs. By ignoring some of the human genes in many_human_genes-to-one_fly_gene relationships, I suspect we have under reported orthologs relative to the other MODs. I am happy to revisit our calls based on whatever consensus the project agrees but given the lack of time, the gene target numbers may need to be reviewed.<br />
<br />
<br />
== RGD Orthology Determination Method ==<br />
<br />
RGD has been providing information on the homologous mouse and human genes for quite some time. <br />
<br />
All homology information and relationships are based on the mouse/human/rat sets that MGI puts together and makes available on their ftp site. Detailed infomation is found at MGI's entry on this page.<br />
<br />
Comment: occasionaly, it is possible to find entries for the homologous genes but nor for the rat gene becuase of some delayes in loading rat information from Entrez Gene. However, all our pipelines have been updated and expanded and will be working on a regular basis.</div>Vpetri