*is there any way to avoid explosuion of classes with medication adminsitration? **pre composed vs post composed ** document deisgn logic
** implement details fort AAML
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review line and treatment exposure
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Look at medication sigs to implement key componets ** dose ** dose unit ** schedule ** frequency ** Route ** cyclesigs
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continue modeling aaml https://hemonc.org/wiki/Acute_myeloid_leukemia,_pediatric#COG_AAML1031_arm_C_.28FLT3.2FITD.2B.29
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Work on automation of scraping.
DONE
- add names for protocols and regimens name property
- haspublication
- publication - has DOI
- look at duration property - subpropoerties hasduration days has duration weeks.
- can i find an example of a course with cycles?
- mail jeremy
dropbox/list of questoins ?
- definitions
- troble running code
- reviewing which is the protocol/course/regimen
- list of phases?
- treatment context -hasLine, has Phase-
- add a diagnosis - associated with a protocol
add subclasses of medication administration for local anticancer supportive
- treatment context -hasLine, has Phase-
If it is intended to be given once, but might be repeated, it is a course. A regimen that occurs in isolation is stand-alone,
-treatmentList hasTreatment someTreatment (exactly1) treatmentList hasPhase somePhase (exactly 1) protocol has treatment list model regiment with types of medication adminsistration. anticancer local supportive treatment modality `
- regimen
- phase
- protocol definition
- line definition* phase, line, protocol, regimen relations
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review of definitions of regimen, protocol, line, intent...
flesh out line
-mail jeremy are phasess asoociated with reigmens? Lines? If we downplay protocol, where do phases fit itn ? depreate treatment contesxt *** notes on open questions **heck status in github - commit and backup
- check haspriortherapy - domain and range?
- add Line
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remove medicaiton administration.
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put lists in regimen for treatment
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protocol as ordered list? -make treatment list refer to these
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add subclasses
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clean names of phases.
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add study protocol with DOI. https://www.researchgate.net/publication/351037551_A_Practical_Guide_to_Building_OWL_Ontologies_Using_Protege_55_and_Plugins - diagnsois name and coee? clean up definitions
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order phases https://www.cancerresearchuk.org/about-cancer/acute-lymphoblastic-leukaemia-all/treatment/phases Should specific phases (Inductino, etc. be individuals? Look at pizza? yes. add these * pre-phase/pre-induction -induction subsequent *induction - consolidation subsequent *consolidation - intensification *intensification - maintenance *maintenance interim_maintenance adjuvant - maintenance neoadjuvant -definitive definitive -adjuvant delayed intensification continuation salvage upfrontinductiontherapy
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work on ordering of phases? **How do i say that induction may be followed by either intensification or consoolidation?
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add cancer, cns, and locall subytypes of administration to medication administartion
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add these administrations to regiemn
- move away from medication categories - all medications should be in one list. we will use medicationadministration catgories to indicate how each drug is used in a given protocol.
- what about the instances of AAML_1031_ARMC_C , etc.? - yes. remove these instances
- should we remove the explicit instances of medication administration? yes
- run pellet and look at reasoning errors.a
- remove instances *** correct url -- currently prefix is off. Can I fix that? -edit file ** some problem with 000075 000099 - hasDOI? has publication?
- aplenc has Doi...10.3324/haematol.2019.220962 *** fix 0000075 - cardinality *** re-add publication and has doi ** some problem with 000075 000099 - hasDOI? has publication?
- aplenc has Doi...10.3324/haematol.2019.220962 *** fix 0000075 - cardinality *** re-add publication and has doi <<<<<<< HEAD =======
- review structure as compared to midas data or others ** re-add has duration, DONE
- review structure as compared to midas data or others ** hasDose ** hmm. having duration in instances is not working well. Deal with instances asnd turn them to classes? ** review other structures of inheritance. *** regimens being subclass of parts pr phases *** others?
75876c8 (further cleanup)
- populate the induction, intensification, etc. from AAML with meds and administration.
- fix the PIZ - named classes.