GO Curation For Beginners , and leads you through the steps that must be taken to address a single Sourceforge request. GO SourceForge curator request tracker is a web page showing a list of the requests for changes to the ontologies that have been made. To claim a request you should log in and click on the summary hyperlink part of the request line. Then change the 'Group' menu to 'GO', and the 'assigned to' menu to your own initials. Press 'submit changes' to update the web page and then have a think about what you will do to fulfill the requirements of the request you have claimed e.g. add terms as requested. If you want to find out how to word a definition or term name then look at the Curators' Guide to GO Style
cvs loginIt'll ask you for your password (which you should have got from Mark Schroeder) Then to update the copies of the ontology and definitions files on your computer type the command:
cvs updateIf you are in a different directory you can type the same command followed by the pathname to produce the same effect. To update only a subset of the files you can type a more specific pathname, for example:
cvs update go/ontology/
Next you should give the command
to copy all three ontologies and the defs into the directories called 'old' that you have created in your 'doc' and 'ontology' directories. Once this is complete you can load the files into DAG-Edit.
%term name ; GO:nnnnnn %term name ; GO:nnnnnn <term name ; GO:nnnnnn <term name ; GO:newIn this system the '%': character indicates an is_a relationship, whilst the < character indicates a part_of relationship.
Users/yourname/Documents/go/ontologyAlso set the path for the definitions file:
Users/yourname/Documents/go/docYou'll only have to set these paths once. When set, save the files by ticking the 'Use legacy compatible types' box, and then clicking the 'Save GO flat files' button at the bottom of the DAG-Edit screen.
Once you've finished working, you can commit your revisions to the repository at Stanford. Before you do this, check that you've done what you think you've done by comparing the edited version with your previous version. Note that for the following commands you can use UNIX aliases, such as those suggested in the Beginners' Guide to Modifying the Ontologies. First you must compare your modified files with the unmodified files to check the changes that have been made are the ones you are expecting. If you've just edited the process ontology, for example, compare your tempfile with the previous version by typing
diff go/ontology/process.ontology go/ontology/old/process.ontology (alias: dp)If you have modified any of the other files then you should also check those individually by using the relevant command:
diff go/ontology/function.ontology go/ontology/old/function.ontology (alias: df) diff go/ontology/component.ontology go/ontology/old/component.ontology (alias: dc)If you've edited any definitions, you should also compare the GO.defs files:
diff go/doc/GO.defs go/doc/old/GO.defs (alias: dd)At this stage you can also open the modified files in emacs to check for extra spaces and newline characters. To search for newlines type:
ctrl-s \n RETDelete any newline characters and then repeat the search for extra spaces:
ctrl-s [press space bar twice] RETOnce you're happy that the files have been changed in exactly the way that you expected them to have changed, (get someone to check the first few times) check them against the current versions in the cvs repository: To do this you need to use the following aliases which give the commands shown in inverted commas after them:
To check the component ontology file against the current version in the cvs repository
dcvsc 'cvs -d :pserver:firstname.lastname@example.org:/share/go/cvs diff go/ontology/component.ontology | more'
To check the function ontology file against the current version in the cvs repository
alias dcvsf 'cvs -d :pserver:email@example.com:/share/go/cvs diff go/ontology/function.ontology | more'
To check the process ontology file against the current version in the cvs repository
alias dcvsp 'cvs -d :pserver:firstname.lastname@example.org:/share/go/cvs diff go/ontology/process.ontology | more'
To check the definition file against the current version in the cvs repository
alias dcvsd 'cvs -d :pserver:email@example.com:/share/go/cvs diff go/doc/GO.defs | more'
When you do this you will probably see just the changes that you have made, but if someone else has also commited changes since you last updated then you will see those too. If you see changes that you did not make then you will have to carry out
again to merge the current cvs version with your working files. You can also update the individual files separately:
cvs update [pathname]for example:
cvs update go/ontology/process.ontology (alias: upp) cvs update go/ontology/component.ontology (alias: upc) cvs update go/ontology/function.ontology (alias: upf) cvs update go/doc/GO.defs (alias: upd)or
cvs update [updates all files]This will check your version of the file in your working directory against the version in CVS and tell you if someone else has changed the same parts as you have changed. If only two different parts have been changed then the files will be merged to include both sets of changes. Ask someone to watch for any error reports, e.g. spaces that you have left where they should not be. A capital 'M' will show if all is well, and a capital 'C' if there are problems. You can then commit your changes to the CVS repository in Stanford:
cvs ci go/ontology/process.ontology (alias: cvsp) cvs ci go/ontology/component.ontology (alias: cvsc) cvs ci go/ontology/function.ontology (alias: cvsf)If you've edited the definitions file, type
cvs ci go/doc/GO.defs (alias: cvsd)After you have committed a file, an emacs window will pop up prompting you to add a comment on how you've changed the files. Type what you've done (this can be pasted from the history plugin in DAG-Edit or from the Text Edit file you made earlier). You should also include the reasoning behind your decisions. Then type ctrl-x ctrl-s to save the CVS log file, and then ctrl-x ctrl-c to exit it.
After you have committed a file, check each of the relevant log files to make sure that the right number of lines has been edited (As before, only check the biological process, molecular function and cellular compnent ontology files if you have worked on them, and only check the definitions file if you have altered or added any definitions.)
cvs log go/ontology/process.ontology | more (alias: logp) cvs log go/ontology/function.ontology | more (alias: logf) cvs log go/ontology/component.ontology | more (alias: logc)'| more' sends the log's contents through the UNIX 'more' utility, which allows you to view it a page at a time. Press 'q' to quit.
*This is a technical bit where it is better to ask for help*
Ask someone to check the log file, and look out for characteristics shown in this explanation of what is going on:
The top of the log file will say something like (on a single line):
revision 2.480 date: 2002/07/15 21:51:02; author: berardini; state: Exp; lines: +1018 -262
The difference between +1018 and -262 is the number of lines that have been edited. If, for example, you had edited only a couple of terms and you got these numbers, you'd know that something had gone awry. If this is the case and you can't work out what has caused the differences, the safest thing to do is restore the previous version. If the current version is 2.480, the following command to checkout version 2.479:
cvs co -p -r 2.479 go/ontology/process.ontology > old_process
The -p -r command checks out the file without sticky tags, which cause strange things to happen to the file. '>old_process' just saves version 2.479 as a file called old_process. Once you've checked out the old version, use it to overwrite your working version:
cp old_process go/ontology/process.ontology
You can now commit the old version as usual.
*Back to easy stuff again now*
Every time you add a new term to the ontology you also create a record of what it is in the GO numbers file. To open this file in emacs type
emacs go/numbers/go_numbers (alias: en)
You can add each new GO term as you work or paste the final set of information from your TextEdit file.
You must also commit the numbers file to CVS by typing:
cvs ci /go/numbers/go_numbers (alias: cvsn)
If you have added synonyms then you must also update the synonym file.
If someone else has committed files in between your last CVS update and your attempt to commit your updated files, the following message will appear in your terminal window:
CVS server: Up-to-date check failed for `go/ontology/process.ontology' CVS [server aborted]: correct above errors first! CVS commit: saving log message in /tmp/CVS000388
When this occurs, you need to merge the latest version in the repository with your working file. First, perform the CVS update command on the relevant file, to merge your working version with the current version in the repository. At this point you might get the following message:
RCS file: /share/go/CVS/go/doc/GO.defs,v retrieving revision 2.646 retrieving revision 2.650 Merging differences between 2.646 and 2.650 into GO.defs rcsmerge: warning: conflicts during merge cvs server: conflicts found in go/ontology/process.ontology C go/ontology/process.ontology
You need to correct the conflicts before committing your working version. Open the working version (not the temp version) of whichever file has failed to commit and use the ctrl-s command to search for the following text strings:
>>> <<< ====
These characters appear when the same part of the file has been edited in both versions; <<< and >>> bracket the part that's been edited, and ==== underlines the part where there are conflicts. The most common type of conflict is in the header and in this case you need to decide which form of the header to keep, and then delete the other form and all of the conflict characters. If you find conflict characters within a new term then find its associated GO-ID and search for other instances of it (usually they're next to each other). Once you've found two or more terms with the same ID, you'll have to decide which one is correct and delete the other one (ctrl-k allows you to delete a line at a time). When you've deleted all the conflicts, save it, close it, and commit your edited working version.
After you have committed the file, check the log file, as described above, to make sure that the right number of lines has been edited. Occasionally, when you try to commit files you'll get the message
Waiting to obtain lock.
This means that someone else is committing a file. You simply have to leave this running in the background until the other person has finished committing his/her file.
An e-mail will now be sent to the person who logged the request and to you, containing the contents of the comments field.
If you are learning to curate using this web page and you find out things that you think should be included then you can contribute to it by e-mailing the webmaster. Until all these helpful nuggets of advice have been put together in coherent form they will be stored in 'random accumulated helpful advice for curators'.
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