Style Guide Notes

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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.
   

ID space:

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]
   samples:

Dengue:

   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.


Definition Guidelines:

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″
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