Releases/2009-11-06/Cleanup log

Alan, working on editor note cleanup.

Checking that the editor notes that just have msi ids all have appropriate definition sources
(sparql '(:select (?term ?source ?val) (?term !obo:IAO_0000116 ?val) (:optional (?term !obi:IAO_0000119 ?source)		   (:filter (and (regex (str ?source) (str ?val)) (regex (str ?source) "http://msi-ontology.sourceforge.net/ontology/\\S+.owl#")))) (:filter (and (regex (str ?val) "msi_") (not (bound ?source)))))		 :use-reasoner :none :kb kb :trace t)

PREFIX obi:  SELECT ?term ?source ?val WHERE { ?term obi:IAO_0000116 ?val. ?term rdfs:label ?label. OPTIONAL {       ?term obi:IAO_0000119 ?source. FILTER (regex(str(?source),str(?val)) &&              regex(str(?source),"http://msi-ontology.sourceforge.net/ontology/\\S+.owl#")) }.  FILTER (regepx(str(?val),"msi_") && (!(bound(?source))))}

Results: !obi:OBI_0000628	"carbon nanotube column"	NIL	"msi_01107"

Various other issues that surfaced during editor notes review

 * Found missing manufacturers Tracker 2887864
 * Found over-generic labels Tracker 2887868
 * Found empty properties Tracker 2887874
 * Found duplicate - adjuvent role, adjuvant role Tracker 2887909
 * Found "played" roles - Tracker 2887917
 * Found editor notes that say "RESOLVE:" Tracker 2887932
 * Found dubious subclasses of documenting Tracker 2887974
 * DS questions about whether terms are justified Tracker 2888194
 * Entity of organismal origin mentions Tracker 2888194

DONE:
 * Asked Jennifer about roles that have CDISC definitions in editor notes Tracker 2889625
 * Poor label 'image stream' Tracker 2888037
 * Found "to be added" examples of usage. Tracker 2887965
 * Found classes below obsolete_under_discussion Tracker 2888484
 * Found non obsolete obsolete_hyphenated NMR instrument platform Tracker 2888481
 * Found "source pending" definition sources - Tracker 2887928

[[media:editor-notes-mc.txt]]

What was done to editor notes

 * All editor notes were reviewed and categorized into several categories by Alan. Melanie reviewed and made some changes, almost all of which were accepted. The results are in the columns "disposition" (alan's) and "disposition 2" (melanies).
 * "check" - a tracker item will be entered
 * "ignore" - is ignored already
 * "definition editor" - misplaced definition editor
 * "todo" - a tracker item will be entered
 * "obsolete" - an obsolete term
 * "asked philippe" - editor notes "MO" or "MSI" - he said to delete
 * "asked jennifer" - CDISC definitions
 * "separate" - put in a separate file (not for release)
 * "user" - possibly of interest to user
 * "delete" - obsolete note


 * Those editor notes marked "separate" "check" "todo" "asked jennifer" were changed into "curator note" annotations. If there was a mark in "disposition 2" it was preferred over whatever was in "disposition".
 * Those marked "user" were left as editor notes
 * All other notes were discarded.

All are currently in the single obi file. Curator notes will not be included in release.

(misc notes)


 * Fixed definition source for carbon nanotube column
 * Deleted all msi_xxx editor notes
 * Marked all editor notes on obsolete terms as "obsolete". Ignore these and just move them to obsolete file when we do obsoletes.
 * Marked all NMR
 * Marked all alanr notes "this should be moved to obi" as "delete"
 * Marked all "NMR" notes as "separate" = keep in separate file
 * Asked Philippe about "MSI" note on fractional factorial design OBI_0500016 (+ others marked "ask philippe") - He says delete.

Preferred labels
I reviewed all the cases where a current editor preferred label differed from an rdfs:label, and classified them into 4 cases.


 * "e": the preferred label is in fact an example of usage. I fixed this in the obi source file
 * "f": The rdfs:label had a typo in it. I fixed the rdfs:label in the obi source file and ignored the editor preferred label
 * "n": The editor preferred label is not an alternative term. I discarded it when generating the release. These currently are maintained in the obi source file but will be removed if there is not disagreement on my assessments.
 * "y": The current editor preferred label looks like a reasonable alternative term. I fixed these in the obi source file. If there is disagreement about any of these please put in a ticket.

Here's the query I used to get the initial list:

PREFIX obi:  PREFIX rdfs:  SELECT ?term ?label ?preflabel WHERE { ?term rdfs:label ?label. ?term obi:IAO_0000111 ?preflabel. FILTER ((!((str(?label) = str(?preflabel)))) && (!(regex(str(?label),"obsolete"))) && regex(str(?term),"OBI_"))}

e OBI_0000006	"role of being consumer safety officer"	"Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm" e OBI_0000824	"recombinant YAC cloning"	"Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21"

f OBI_0000056	"Notified_Body role"	"Notified Body" f OBI_0000395	"signal amplifcation function"	"signal amplification function" f OBI_0000398	"image aquisition device"	"image acquisition device" f OBI_0600026	"longitundinal mass measurement assay"	"longitudinal mass measurement assay"

n OBI_0000014	"regulator role"	"Regulator" n OBI_0000016	"regulation-assigned role"	"Regulation-assigned role" n OBI_0000017	"regulatory role"	"Regulatory role" n OBI_0000018	"supplier role"	"Supplier" n OBI_0000020	"contract research organization role"	"Contract research organization" n OBI_0000025	"reference substance role"	"Reference substance" n OBI_0000026	"cytological stain role"	"Cytological stain" n OBI_0000032	"clinical research coordinator role"	"Clinical research coordinator" n OBI_0000040	"drug role"	"Drug role" n OBI_0000060	"trial monitor role"	"Trial monitor" n OBI_0000064	"positive reference substance role"	"Positive reference substance" n OBI_0000068	"reporting party role"	"Reporting party" n OBI_0000079	"culture medium role"	"Culture medium" n OBI_0000089	"role of regulator of chemical manufacture"	"Regulator of chemical manufacture" n OBI_0000092	"role of certified IRB professional"	"Certified IRB Professional" n OBI_0000093	"patient role"	"Patient" n OBI_0000100	"role of being first subject treated"	"First subject treated" n OBI_0000102	"responsible party role"	"Responsible party" n OBI_0000103	"principal investigator role"	"Principal investigator" n OBI_0000110	"pH indicator dye role"	"pH indicator dye" n OBI_0000116	"worker role"	"Worker" n OBI_0000117	"bernoulli trial"	"Bernoulli trial" n OBI_0000140	"label role"	"Label" n OBI_0000143	"baseline participant role"	"Baseline participant" n OBI_0000144	"role of independent data monitoring committee"	"Independent data monitoring committee" n OBI_0000145	"pathologist role"	"Pathologist" n OBI_0000154	"role of Institutional Review Board"	"Internal Review Board" n OBI_0000161	"crossover population role"	"Crossover population" n OBI_0000162	"complete nutrient role"	"Complete nutrient" n OBI_0000163	"radiolabel role"	"Radiolabel" n OBI_0000169	"placebo role"	"Placebo" n OBI_0000174	"study group role"	"Study group population" n OBI_0000188	"role of pathology review board"	"Pathology review board" n OBI_0000196	"role of impartial witness"	"Impartial witness" n OBI_0000198	"biological replicate role"	"Biological replicate" n OBI_0000204	"nutrient role"	"Nutrient" n OBI_0000205	"dropout role"	"Dropout" n OBI_0000207	"health care provider role"	"Health care provider" n OBI_0000211	"proxy respondent role"	"Proxy respondent" n OBI_0000214	"negative reference substance role"	"Negative reference substance" n OBI_0000215	"role of legally acceptable representative"	"Legally acceptable representative" n OBI_0000220	"reference subject role"	"Reference participant" n OBI_0000221	"vital dye role"	"Vital dye" n OBI_0000223	"blinded medication role"	"Blinded medication" n OBI_0000224	"sub-investigator role"	"Sub-investigator" n OBI_0000234	"trial statistician role"	"Trial statistician" n OBI_0000237	"antigen role"	"Antigen" n OBI_0000243	"sponsor role"	"Sponsor" n OBI_0000248	"feed role"	"Feed" n OBI_0000249	"technical replicate role"	"Technical replicate" n OBI_0000250	"dye role"	"dye" n OBI_0000273	"role of regulator of consumables and medical devices"	"Drug regulatoy authority" n OBI_0000399	"immobilize function"	"immobilize funtion" n OBI_0000520	"clinical chemistry assay"	"detection of analyte in blood sample" n OBI_0200064	"centroid mass spectrum"	"centroid mass spectrun" n OBI_0200083	"survival analysis objective"	"survival analysis" n OBI_0200091	"determining inter-rater agreement"	"inter-rater agreement" n OBI_0302731	"buffer role"	"buffer" n OBI_0400013	"band pass filter"	"band_pass_filter" n OBI_0400024	"CyFlow SL"	"CYFlow SL" n OBI_0400043	"flow cell"	"flow_cell" n OBI_0400045	"fluid pressure regulator"	"fluid_pressure_regulator" n OBI_0400047	"gas laser"	"gas_ aser" n OBI_0400081	"particle delivery vessel"	"particle_delivery_vessel" n OBI_0400085	"piezo electric crystal"	"piezo_electric_crystal" n OBI_0400100	"syringe pump"	"syringe_pump" n OBI_0400102	"waste tank"	"waste_tank" n OBI_0400140	"gel tank"	"gel_tank" n OBI_0600028	"artificially induced reverse transcription"	"artifically induced reverse transcription" n OBI_0000086	"reagent role"	"Reagent" n OBI_0400080	"optical subsystem"	"optical_subsystem"

y OBI_0600040	"synthesis"	"synthesize" y OBI_0000470	"mass spectrometry assay"	"mass spectrometry" y OBI_0000801	"spike train datum"	"spike train measurement" y OBI_0000807	"presentation of stimulus"	"stimulation of organism" y OBI_0000816	"micro electrode"	"micro electrode measuring device" y OBI_0200034	"jackknifing method"	"jackknifing" y OBI_0200089	"multiple testing correction method"	"multiple testing procedure" y OBI_0200098	"soft independent modeling of class analogy analysis"	"SIMCA" y OBI_0200111	"data visualization"	"visualization" y OBI_0600016	"pooling material from organisms"	"material pooling" y OBI_0600031	"ELISPOT assay"	"ELISPOT" y OBI_0600048	"vector mediated amplification"	"amplification of a clone" y OBI_1110132	"CD8 receptor"	"CD8" y OBI_0000202	"investigation agent role"	"Personnel role"

There are minor changes from the above noted in Tracker 2893997

Spelling corrections
"ploymerization" -> polymerization "decompostion" -> decomposition "extration" -> extraction "outputing" -> outputting "combininig" -> combining "charactreristic" -> characteristic "flourescent" -> fluorescent "inputing" -> inputting "emmitted" -> emitted "subsytem" -> subsystem "choise" -> choice "matterial" -> material "may may" -> map "iin" -> in "microtitre" -> microtiter "partical" -> particle "functionto" -> function to "dectors" -> detectors "entitiy" -> entity "disolved" -> dissolved "emmission" -> emission "process,the" -> process, the "transformationi" -> transformation "passiv," -> passive, "powerfull" -> powerful "adminstration" -> administration "viceversa" -> vice versa "speciment" -> speciment "subjeceted" -> subjected "ie" -> i.e. "occurence" -> occurrence "portionn" -> portion "portio" -> portion "enabeling" -> enabling "indegree" -> in-degree "outdegree" -> out-degree "aquire" -> acquire "aquisition" -> acquisition "extraneuous" -> extraneous "differrent" -> different "quantom" -> quantum "wih" -> with "partioning" -> partitioning "carrie" -> carry "chromaptgraphy" -> chromatography "dicusssion" -> discussion "multicelluar" -> multicellular "arive" -> arrive "volatalization" -> volatilization "calulcation" -> calculation "introcue" -> introduce "GenePatter" -> GenePattern "nmr" -> NMR "environmentl" -> environmental "binarydigital" -> binary digital "biais" -> bias "datapoints" -> data points "exmination" -> examination "repliccate" -> replicate "crystaline" -> crystalline "flashlamp" -> flash lamp "assymetric" -> asymmetric "consituant" -> constituent "detoxification,hemotapoeietic" -> detoxification, hemotapoeietic "proceses" -> processes "widebore" -> wide bore "ocurring" -> occurring "possiby" -> possibly "the the" -> the "enitity" -> entity "assymmetric" -> asymmetric "modelling" -> modeling "froma" -> from a "polynommial" -> polynomial "continuos" -> continuous "colum" -> column "metalic" -> metallic "An cation" -> A cation "cristal" -> crystal "irratidates" -> irradiates "cyttometer" -> cytometer "relaized" -> realized "nuceic" -> nucleic "digitiesed" -> digitized "consumableis" -> consumable is "bearning" -> bearing "recominant" -> recombinant "moleculeany" -> molecule any "detecor" -> detector "alalog" -> analog "diffusiton" -> diffusion "inpact" -> impact "lourescent" -> fluorescent "emmited" -> emitted "focussing" -> focusing "separateion" -> separation "freqeuntly" -> frequently "nitorgen" -> nitrogen "anaylsis" -> analysis "confered" -> conferred "vetcor" -> vector "odf" -> of "cromatography" -> chromatography "independant" -> independent "diagnsis" -> diagnosis "oestrogen" -> estrogen "investivation" -> investigation "organislm" -> organism "synthezised" -> synthesized "mixttures" -> mixtures "indefinately" -> indefinitely "hiearchical" -> hierarchical "clustring" -> clustering "trancsripts" -> transcripts "calulcation" -> calculation "fluorescnce" -> fluorescence "pulsewidths" -> pulse widths "synringe" -> syringe "connected,attached" -> connection, attached "ouput" -> output "conmtains" -> contains "files.They" -> files. They "hierarchicaly" -> hierarchically "inividal" -> individual "artifical" -> artificial "materila" -> material "outpu" -> output "flouresce" -> fluoresce "availalbe" -> available "tthat" -> that "ultaimtely" -> ultimately "gaz" -> gas "FIlters" -> Filters "acidsl" -> acids "bandpass" -> band-pass "insturment" -> instrument "proprty" -> property "wellplate" -> well plate "hastaloy" -> hastelloy "photodector" -> photodetector "cells.This" -> cells. This "interogation" -> interrogation "occurent" -> occurrent "parametersand" -> parameters and "nonrepeatable" -> non-repeatable "artifically" -> artificially "specifc" -> specific "Differrences" -> Differences "affinnity" -> affinity "seive" -> sieve "proprotion" -> proportion "conainted" -> contained "celll" -> cell "in heres" -> inheres "artefact" -> artifact "constituants" -> constituents "tissues.Values" -> tissues. Values "occuring" -> occurring "concretisation" -> concretization "measuremeant" -> measurement "electropheris" -> electrophoresis "fiberoptics" -> fiber optics "approximateed" -> approximated "comparewd" -> compared "logicle" -> logical "aggegration" -> aggregation "differntial" -> differential "collector.Guava" -> collector. Guava "acomplish" -> accomplish "techique" -> technique "dischargeing" -> discharging "amplication" -> amplification "assayis" -> assay is "distriubition" -> distribution "colelction" -> collection "aplications" -> applications "oragnism" -> organism "reproter" -> reporter "strucure" -> structure "techically" -> technically "mutation,deletion" -> mutation, deletion "proportioal o" -> proportional to "intermitent" -> intermittent "realtime" -> real time "hightest" -> highest "recieves" -> receives "implict" -> implicit "anlysis" -> analysis