Style Guide Notes
Thoughts on the scope of DO:
From discussions between Saul, Warren, Lynn: A disease ontology describing the mechanisms of acquisition and the spectrum of 'typical' manifestations.
UMB DOID:$sequence(7,50000,50999)$ [Suvi] UMB DOID:$sequence(7,60000,60999)$ [Lynn] Northwestern DOID:$sequence(7,70000,70999)$ [LaRon]
1. Basic guidance
- No plurals - Definition for every term - External references including URLs for the definitions - Any obsoleted term should have external references moved to closest remaining term
2. Example Definition
Here is a breakdown of the format of the Disease Ontology definition format:
A disease that is A disease that involves A disease that is manifested in
The first sentence should describe: the disease involves .... "these conditions, signs, symptoms". headache, severe joint pain and a rash. The second second sentence: additional symptoms, if needed. The third sentence: the etiology: the cause of the disease e.g. dengue viruses [NCBITaxon:12637] transmission, e.g. vector: transmitted by mosquitoes of the genus Aedes [NCBITaxon:7158]
A flavivirus infection that involves headache, severe joint pain and a rash. Dengue viruses [NCBITaxon:12637] are predominantly transmitted by mosquitoes of the genus Aedes [NCBITaxon:7158].
DHF: Dengue Hemorrhagic Fever A dengue that involves a shock-like state marked by hemorrhagic symptoms such as hemorrhagic lesions of the skin, thrombocytopenia, and reduction in the fluid part of the blood. DHF presents as the result of a second dengue virus infection.
DSS: Dengue Shock Syndrome
A dengue that is the most severe form of dengue fever accompanied by circulatory collapse, involves hypotension, narrow pulse pressure (less than or equal to 20mm Hg), or frank shock. The shock occurs after two to six days of symptoms, followed by collapse, weak pulse, and blueness around the mouth. Symptoms also include: easy bruising, blood spots, bleeding gums and nosebleeds. Dengue shock syndrome can be fatal. The mortality rate ranges from 6 to 30 percent, most commonly in children.
Chris's comment's last night: The policy in GO (which is still not yet uniformly implied) is to put the superfluous tidbits (which are very useful) after the first period. The part before the full-stop is the formal definition, the part after is the additional descriptive text. Ideally these would go in separate controlled fields but that's not really how it evolved.
3. Example XRefs, synonyms
[Term] id: DOID:612 name: immunologic deficiency syndrome synonym: "hypoimmunity" EXACT [CSP2005:1553-9570] synonym: "immune deficiency disorder" EXACT [CSP2005:1560-5885] synonym: "Immunodeficiency" EXACT [NCI2004_11_17:C39725] synonym: "Immunodeficiency (disorder)" EXACT [SNOMEDCT_2005_07_31:64431000] synonym: "Immunodeficiency disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:234532001] synonym: "immunodeficiency syndrome" EXACT [NCI2004_11_17:C3131] synonym: "Unspecified immunity deficiency" EXACT [ICD9CM_2006:279.3] synonym: "Unspecified immunity deficiency (disorder)" EXACT [SNOMEDCT_2005_07_31:191005003] xref: GeneRIF:11466342 xref: GeneRIF:11779494 xref: GeneRIF:11836625 xref: GeneRIF:11862382 xref: GeneRIF:12133934 xref: GeneRIF:12353035 xref: GeneRIF:12421939 xref: GeneRIF:12444103 xref: GeneRIF:12469117 xref: GeneRIF:15100680 xref: GeneRIF:15128795 xref: GeneRIF:15356572 xref: GeneRIF:15696198 xref: GeneRIF:15699179 xref: GeneRIF:15781335 xref: GeneRIF:15781580 xref: GeneRIF:15965469 xref: ICD9CM_2006:279.3 xref: MSH2005_2005_01_17:M0011155 xref: MSH2006_2005_11_15:D007153 xref: NCI2004_11_17:C3131 xref: NCI2004_11_17:C39725 xref: SNOMEDCT_2005_01_31:191005003 xref: SNOMEDCT_2005_01_31:234532001 xref: UMLS_CSP2004_AUI:A0319259 xref: UMLS_CSP2004_AUI:A1305419 xref: UMLS_CSP2004_AUI:A1307271 xref: UMLS_CUI:C0021051 xref: UMLS_ICD9CM_2005_AUI:A0271927 xref: UMLS_ICD9CM_2006_AUI:A8344021 xref: UMLS_MSH2005_2005_01_17_AUI:A0045862 xref: UMLS_MSH2005_2005_01_17_AUI:A0045863 xref: UMLS_MSH2005_2005_01_17_AUI:A0045865 xref: UMLS_MSH2005_2005_01_17_AUI:A0045866 xref: UMLS_MSH2005_2005_01_17_AUI:A0072557 xref: UMLS_MSH2005_2005_01_17_AUI:A0072559 xref: UMLS_MSH2005_2005_01_17_AUI:A0072603 xref: UMLS_MSH2005_2005_01_17_AUI:A0072604 xref: UMLS_MSH2005_2005_01_17_AUI:A0122028 xref: UMLS_MSH2005_2005_01_17_AUI:A0122029 xref: UMLS_MSH2005_2005_01_17_AUI:A0122176 xref: UMLS_MSH2005_2005_01_17_AUI:A0122177 xref: UMLS_NCI2004_11_17_AUI:A7575638 xref: UMLS_NCI2004_11_17_AUI:A7581099 xref: UMLS_NCI2004_11_17_AUI:A7584546 xref: UMLS_NCI2004_11_17_AUI:A7600703 xref: UMLS_NCI2004_11_17_AUI:A7600707 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A2892046 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3033331 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3144216 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3144217 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3505469 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3772213 xref: UMLS_ST:T047 is_a: DOID:2914 ! immune system disease
4. Example of an obsolete term due to not being a disease
[Term] id: DOID:1000 name: Uterine Rupture synonym: "Rupture of uterus (disorder)" EXACT [SNOMEDCT_2005_07_31:34430009] synonym: "Ruptured uterus" EXACT [SNOMEDCT_2005_07_31:156231001] xref: MSH2005_2005_01_17:M0022435 xref: MSH2006_2005_11_15:D014597 xref: UMLS_CUI:C0042143 xref: UMLS_MSH2005_2005_01_17_AUI:A0113357 xref: UMLS_MSH2005_2005_01_17_AUI:A0113369 xref: UMLS_MSH2005_2005_01_17_AUI:A0130889 xref: UMLS_MSH2005_2005_01_17_AUI:A0130890 xref: UMLS_ST:T047 is_obsolete: true
5. Example of an obsoleted term that may need to be re-added. Lots of nice xrefs to add back at the very least! [is obsolete as of svn revision 73, August 4, 2009]
[Term] id: DOID:10037 name: Pilonidal Sinus synonym: "Cyst - pilonidal" EXACT [SNOMEDCT_2005_07_31:302224009] synonym: "Cyst - pilonidal (disorder)" EXACT [SNOMEDCT_2005_07_31:47639008] synonym: "Pilonidal cyst" EXACT [ICD9CM_2006:685] synonym: "Pilonidal Cyst" EXACT [MTH:NOCODE] synonym: "Pilonidal sinus" EXACT [SNOMEDCT_2005_07_31:302223003] synonym: "Pilonidal sinus/cyst" EXACT [SNOMEDCT_2005_07_31:156320006] synonym: "Pilonidal sinus/cyst" EXACT [SNOMEDCT_2005_07_31:200711002] synonym: "Pilonidal sinus/cyst" EXACT [SNOMEDCT_2005_07_31:267837002] synonym: "Pilonidal sinus/cyst NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:200716007] xref: ICD9CM_2005:685 xref: MSH2005_2005_01_17:M0016864 xref: MSH2006_2005_11_15:D010864 xref: SNOMEDCT_2005_01_31:200716007 xref: SNOMEDCT_2005_01_31:47639008 xref: UMLS_CUI:C0031925 xref: UMLS_ICD9CM_2005_AUI:A0446858 xref: UMLS_MSH2005_2005_01_17_AUI:A0044856 xref: UMLS_MSH2005_2005_01_17_AUI:A0101638 xref: UMLS_MSH2005_2005_01_17_AUI:A0101639 xref: UMLS_MSH2005_2005_01_17_AUI:A0101640 xref: UMLS_MSH2005_2005_01_17_AUI:A0403940 xref: UMLS_MSH2005_2005_01_17_AUI:A0458490 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A2877065 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A2941642 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A2958869 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A2977082 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A2977089 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3058192 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3270621 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3379367 xref: UMLS_SNOMEDCT_2005_01_31_AUI:A3630788 xref: UMLS_ST:T190 is_obsolete: true
Resolving Sourceforge Conflicts-
1) "svn update file" each session you are working. 2) svn commit each time you save your work. 3) resolving svn conflicts
a) When 2 people work on the same file and try to commit their changes, person other than who commited first, will sometimes see "c" as the status of the commit (eg. C HumanDO.obo) or there will be error asking you to update your version (out-of-date). b) Then get the recent version by "svn update" , after that you will find 3 temporary files in your directory. They are, 3 tempoorary files are a) HumanDO.obo.mine(current working copy) b)HumanDO.obo.r1(previous version) c)HumanDO.obo.r2(svn repository version) c) See the conflicts in the txt file by using "emacs HumanDO.obo" command. Delete the header which consists of version information about the recent commit that other person did. And also delete all the other characters like >>>>,<<<<<<<,========. d) Save your file, then use the command "svn resolved HumanDO.obo" . By doing this, you will see that all the temporary files have been erased from your directory. e) Commit your file back to sourceforge using svn -m "......" HumanDO.obo command. f) This gives you clean version on sourceforge with no conflicts.
Respiratory System Infection node
There is an informative and reliable website for curating Thoracic diseases, the link is as follows, http://www.thoracic.org/index.cfm It has the most extensive research information about thoracic diseases and also journals to search.
Merging the versions or Rollback a SVN File By Using Merge
If you have to merge two versions (rollback) due to some reason then follow the steps mentioned in the URL below. http://www.question-defense.com/2008/10/07/rollback-a-svn-file-by-using-merge
In the below example the current SVN revision is 102 and the file was accidentally upgraded to soon from version 101 to version 102.
1. Verify Same File: svn diff -r 102:101 file-name 2. Rollback: svn merge -r 102:101 file-name 3. Verify Change: svn diff -r 102:101 file-name 4. Tell svn Things are OK: svn resolved file-name 5. Checkin File: svn ci file-name -m “rolled back file-name from 102 back to 101″