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G A L E NGALEN-IN-USE: Tools and Methodology Slide 1
Rubrics to Dissections to GRAIL to Classifications
GALEN-IN-USE
A graphical overview of the tools and methodologies being used in the GALEN-IN-USE project to develop a
classification of surgical procedures
The slides in this presentation have accompanying notes. These are visible from the ‘View…Notes Pages’ option on the main PowerPoint menu.
http://www.galen-organisation.com/
http://www.cs.man.ac.uk/mig/galen/
G A L E NGALEN-IN-USE: Tools and Methodology Slide 2
GALEN-IN-USE Partners
University of Manchester, VAMP Health, UK
University of Nijmegen, Holland
EFCC and its affiliates: WCC, NOMESCO, CNR Rome, U St EtienneWCC, NOMESCO, CNR Rome, U St Etienne IASIST, IDGmbH, CMITD, STAKE, U LouvainIASIST, IDGmbH, CMITD, STAKE, U Louvain
University Hospital of Geneva, LNAT, Switzerland
OLE, RAMIT, Datasoft, Belgium
GSF Medis, U Hildesheim, Germany
CNR, Rome, Italy
SPRI, U Linköping, Sweden
VTT, Oulu Univ Hospital, Medici Data, Finland
G A L E NGALEN-IN-USE: Tools and Methodology Slide 3
Surgical
Procedure
Entry
Tool
SPET
ICD
ICPC
SN
OM
ED
G A L E NGALEN-IN-USE: Tools and Methodology Slide 4
RUBRIC "dividing of papillary muscle"CODE "35.31.i1"MAIN dividing
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
Dissection
SPET
G A L E NGALEN-IN-USE: Tools and Methodology Slide 5
RUBRIC "operations on papillary muscle"CODE "35.31"MAIN surgical deed
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
RUBRIC "dividing of papillary muscle"CODE "35.31.i1"MAIN dividing
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
RUBRIC "reattachment of papillary muscle"CODE "35.31.i2"MAIN repairing
ACTS_ON papillary muscleBY_TECHNIQUE reattaching
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
RUBRIC "repair of papillary muscle"CODE "35.31.i3"MAIN repairing
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
‘Sibling’ codes
Dissections
G A L E NGALEN-IN-USE: Tools and Methodology Slide 6
RUBRIC "operations on papillary muscle"CODE "35.31"MAIN surgical deed
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
RUBRIC "dividing of papillary muscle"CODE "35.31.i1"MAIN dividing
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
RUBRIC "reattachment of papillary muscle"CODE "35.31.i2"MAIN repairing
ACTS_ON papillary muscleBY_TECHNIQUE reattaching
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
RUBRIC "repair of papillary muscle"CODE "35.31.i3"MAIN repairing
ACTS_ON papillary muscleHAS_OTHER_FEATURE method VALUE induced arrest of heart
TemplateInterpreterandGRAILGenerator
Dissections
G A L E NGALEN-IN-USE: Tools and Methodology Slide 7
Expansion Algorithm
Map ‘descriptors’Map ‘descriptors’to GRAIL concepts to GRAIL concepts
(usually one-to-one)(usually one-to-one)
Map ‘Links’Map ‘Links’to GRAIL link-concept-link fragmentsto GRAIL link-concept-link fragments
usually one to manyusually one to many
G A L E NGALEN-IN-USE: Tools and Methodology Slide 9
Automatic GRAIL Classification
GALEN Terminology
Server
Browse...
GRAIL
G A L E NGALEN-IN-USE: Tools and Methodology Slide 10
GALEN Terminology
Server
Classification of original rubrics
Browse...
GRAILGALEN
Terminology Server
G A L E NGALEN-IN-USE: Tools and Methodology Slide 11
Different organisationNew organisation calculated automatically, based on the structure provided in the dissection, and in the GRAIL Common Reference Model.
[35.31.i2] is now a child of [35.31.i3], not a sibling (as in the original source).
G A L E NGALEN-IN-USE: Tools and Methodology Slide 12
Browse...
GRAIL
Multilingual Natural Language
DissectionRubric
G A L E NGALEN-IN-USE: Tools and Methodology Slide 13
'037 Biopsie rénale isolée par lombotomie'
SurgicalDeed which isCharacterisedBy (performance whichG isEnactmentOf (BiopsyingProcess whichG < actsSpecificallyOn Kidney hasSpecificSubprocess (SurgicalApproaching whichG hasPhysicalMeans ((Route whichG passesThrough Loin))) >))
en: 'kidney biopsy by lumbotomie'fr: 'biopsie rénale par lombotomie'ge: 'Biopsie der Niere durch Lumbotomie'du: 'biopsie van de nier door lombotomie?'
GRAIL
Multilingual Natural Language
Rubric
Language Generation: example 1
G A L E NGALEN-IN-USE: Tools and Methodology Slide 14
'109 Echographie prostatique transrectale'
SurgicalDeed which isCharacterisedBy (performance whichG isEnactmentOf ((ImagingProcess which playsClinicalRole SurgicalRole) whichG < actsSpecificallyOn ProstateGland hasSpecificPhysicalMeans UltrasonographyMachine hasSpecificSubprocess (SurgicalApproaching whichG hasPhysicalMeans ((Route which hasColinearityWith Rectum))) >))
en: 'transrectal prostate echographie'fr: 'echographie transrectale de la prostate'ge: 'transrektale Sonographie der Prostata'du: 'transrectale echografie van de prostaat'
GRAIL
Multilingual Natural Language
Rubric
Language Generation: example 2
G A L E NGALEN-IN-USE: Tools and Methodology Slide 15
'252 Exérèse d''une tumeur de la glande surrénale à ciel ouvert'
SurgicalDeed which isCharacterisedBy (performance whichG isEnactmentOf ((Excising which playsClinicalRole SurgicalRole) whichG < actsSpecificallyOn (NeoplasticLesion whichG hasSpecificLocation AdrenalGland) hasSpecificSubprocess (SurgicalApproaching whichG hasSurgicalOpenClosedness (SurgicalOpenClosedness whichG hasAbsoluteState surgicallyOpen)) >))
en: 'surgically open extracting of an adrenal gland neoplastic lesion'fr: 'extraction d''une tumeur de la glande surrénale à ciel ouvert'ge: 'offene Extraktion eines Tumors der Nebenniere'du: 'open extractie van een tumor van de bijnier'
GRAIL
Multilingual Natural Language
Rubric
Language Generation: example 3
G A L E NGALEN-IN-USE: Tools and Methodology Slide 16
RUBRIC "valgiserende osteotomie van overig gespecificeerd bot"PARAPHRASE "osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna, without metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot"CODE "5-781.29"ENGLISH_RUBRIC "valgising osteotomy of other specified bone"
MAIN cuttingTO_ACHIEVE Deed:valgising
ACTS_ON Pathology:pathological postureACTS_ON bone
WITHOUT cuttingTO_ACHIEVE Deed:valgising
ACTS_ON Pathology:pathological postureACTS_ON humerus / radius / ulna / femur / tibia / fibula /
os metacarpale / os metatarsale / phalanx
Why Templates?
Small template produces large Grail ...
G A L E NGALEN-IN-USE: Tools and Methodology Slide 17
#printTime.#printMessage 'valgiserende osteotomie van overig gespecificeerd bot'.((SurgicalDeed which <
isCharacterisedBy (performance whichG isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <
hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole) whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Humerus
>))>)extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna,
without metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <isCharacterisedBy (performance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Radius
>))>)
1 2 3 4 5Grail
G A L E NGALEN-IN-USE: Tools and Methodology Slide 18
extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna,
without metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <isCharacterisedBy (performance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Ulna
>))>)extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna,
without metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <isCharacterisedBy (performance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))
1 2 3 4 5Grail
G A L E NGALEN-IN-USE: Tools and Methodology Slide 19
isCharacterisedBy (nonPerformance whichG isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <
hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole) whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Femur
>))>)extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna,
without metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <isCharacterisedBy (performance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Tibia
>))>)extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna,
without metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <isCharacterisedBy (performance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
1 2 3 4 5Grail
G A L E NGALEN-IN-USE: Tools and Methodology Slide 20
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole) whichG
actsSpecificallyOn PathologicalStandingPosture)
actsSpecificallyOn Fibula>))>)extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna, without
metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <isCharacterisedBy (performance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole) whichG
actsSpecificallyOn PathologicalStandingPosture)
actsSpecificallyOn Bone>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole) whichG
actsSpecificallyOn PathologicalStandingPosture)
actsSpecificallyOn Metacarpal>))>)extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna, without
metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <
1 2 3 4 5Grail
G A L E NGALEN-IN-USE: Tools and Methodology Slide 21
isCharacterisedBy (performance whichG isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <
hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole) whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Metatarsal
>))>)extrinsically hasRubric 'valgiserende osteotomie van overig gespecificeerd bot';extrinsically hasParaphrase 'osteotomy of bone with purpose to create a valgising position, without humerus, without radius, without ulna,
without metacarpalen and phalanx of hand, without femur, without tibia, without fibula and without metatarsalen and phalanx of foot';extrinsically hasCode '5-781.29';extrinsically hasEnglishRubric 'valgising osteotomy of other specified bone')extrinsically hasPhysicalSource 'wccfix.txt'.
((SurgicalDeed which <isCharacterisedBy (performance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Bone
>))isCharacterisedBy (nonPerformance whichG
isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG <hasSpecificGoal ((Valgising which playsClinicalRole SurgicalRole)
whichG
actsSpecificallyOn PathologicalStandingPosture)actsSpecificallyOn Phalanx
>))>)
1 2 3 4 5Grail