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Releases: monarch-initiative/MAxO

March 2022 release

31 Mar 19:55
@LCCarmody LCCarmody
v2022-03-31
67356f5
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March 2022 release

Many new terms and updates!

  • ODK 1.3.0 update
  • updated link to the license

New Terms

  • add preimplantation genetic testing
  • add clinical whole genome sequencing and clinical whole exome sequencing
  • add Doppler ultrasonography
  • add fetal echocardiography
  • add botox injection terms
  • add intrauterine fetal transfusion
  • add FAP terms, particularly surgical removal terms
  • add serum alpha-fetoprotein measurement
  • add cognitive assessment branch
  • add copper and iron chelator treatment terms

New Patterns or updates to patterns

  • add new endoscopy pattern
    • add protein ontology import

Other

  • synonym to audiometric procedure
  • add synonyms to echocardiography
    • obsolete fetal Doppler monitoring
  • obsolete Doppler velocimetry
    • update errors in vitamin supplementation/FOODON obsoleted terms
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September 2021 Release

03 Sep 13:43
@LCCarmody LCCarmody
v2021-09-03
3c0f42c
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September 2021 Release

Release updates all 'avoidance patterns' to remove equivalent statements and add the statements as subclasses.
This fixes some erroneous assumptions.

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August 2021 release

16 Aug 17:09
@LCCarmody LCCarmody
v2021-08-16
af84dd7
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August 2021 release

Update slightly protein measurement terms to make sure that all terms are proteins (i.e., bilirubin measurement). Obsoleted MAXO:0000511 Bilevel positive airway pressure ventilation. Created 2 new terms to resolve the issues with similar achronyms. See BiPAP and BIPAP below.

Added new terms:

<style> </style>
MAXO:0000882 behavioral intervention  
MAXO:0000883 cognitive behavior therapy  
MAXO:0000884 behavioral dietary intervention  
MAXO:0000885 surgical removal procedure  
MAXO:0000886 kidney function testing  
MAXO:0000887 glomerular filtration rate test  
MAXO:0000889 renal calculi removal  
MAXO:0000890 calculi removal  
MAXO:0000891 lithotripsy  
MAXO:0000892 renal lithotripsy  
MAXO:0000893 laser lithotripsy  
MAXO:0000894 extracorporeal shock wave lithotripsy  
MAXO:0000895 percutaneous nephrolithotomy  
MAXO:0000896 ureteroscopy  
MAXO:0000897 ureteroscopic stone removal  
MAXO:0000898 purine antagonist agent therapy  
MAXO:0000900 electrocardiography  
MAXO:0000903 aspirin therapy  
MAXO:0000904 alpha-glucosidase inhibitor therapy  
MAXO:0000905 benzodiazepine agent therapy  
MAXO:0000906 T-type calcium channel blocking agent therapy  
MAXO:0000907 L-type calcium channel blocking therapy  
MAXO:0000908 phosphodiesterase inhibitor therapy  
MAXO:0000909 weightloss pharmacotherapy  
MAXO:0000910 anti-obesity agent therapy  
MAXO:0000911 pain management for palliative care  
MAXO:0000912 assessment for sleep disturbance  
MAXO:0000913 sleep assessment questionnarie  
MAXO:0000914 actigraphy  
MAXO:0000915 polysomnography  
MAXO:0000916 airway endoscopy  
MAXO:0000917 placement of a stent  
MAXO:0000918 insertion of a nasopharyngeal stent  
MAXO:0000919 dietician evaluation  
MAXO:0000920 physical therapist evaluation  
MAXO:0000921 respiratory therapist evaluation  
MAXO:0000922 social worker evaluation  
MAXO:0000923 newborn examination  
MAXO:0000924 newborn behavior examination  
MAXO:0000925 Apgar testing  
MAXO:0000926 intrapartum fetal stimulation  
MAXO:0000927 newborn heart rate measurement  
MAXO:0000928 manual fetal rotation  
MAXO:0000929 external fetal rotation  
MAXO:0000930 speech therapy  
MAXO:0000931 psychologist evaluation  
MAXO:0000932 electroencephalography  
MAXO:0000933 enzyme replacement or supplementation therapy  
MAXO:0000934 urine phosphoethanolamine measurement  
MAXO:0000935 bone specific alkaline phosphatase measurement  
MAXO:0000936 alkaline phosphatase enzyme activity test  
MAXO:0000937 inorganic pyrophosphate measurement  
MAXO:0000938 resective brain surgery  
MAXO:0000939 stimulation procedure  
MAXO:0000940 responsive neurostimulation  
MAXO:0000941 extracardiac stimulation  
MAXO:0000942 vagus nerve stimulation  
MAXO:0000943 deep brain stimulation  
MAXO:0000944 cranial electrical stimulation  
MAXO:0000945 spinal cord stimulation  
MAXO:0000946 neurosurgical procedure  
MAXO:0000947 brain surgery  
MAXO:0000948 craniotomy  
MAXO:0000949 calcitonin treatment  
MAXO:0000950 supportive care  
MAXO:0000951 physiological support therapy  
MAXO:0000952 hydration therapy  
MAXO:0000953 saline hydration  
MAXO:0000954 biphosphonate agent therapy  
MAXO:0000955 bi-level positive airway pressure ventilation BiPAP
MAXO:0000956 biphasic positive airway pressure ventilation BiPAP
MAXO:0001176 potassium channel modulator agent therapy  
MAXO:0001177 potassium channel blocker agent therapy  
MAXO:0001178 xanthine oxidase inhibitor agent therapy  
MAXO:0001179 purinergic receptor P2 antagonist agent therapy  
MAXO:0001180 P2Y12 receptor antagonist agent therapy  
MAXO:0001181 serum alkaline phosphatase measurement  
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June 2021 Release

29 Jun 16:12
@LCCarmody LCCarmody
v2021-06-28
a647071
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June 2021 Release

Made several changes to make sure all terms 100% apply to parent terms. If not, new terms were made to reflect proper positioning in the hierarchy (see below).
Also, numerous definitions were added to try to address the Robot report issues.

  • Updated phenotypic abnormality prevention recommendation (vs. phenotypic abnormality avoidance).

  • Made sure that multiple definition errors were correctly labeled as definition and comment (MAXO:0000065, MAXO:0000144)

  • Added definitions for these terms:
    MAXO:0000044
    MAXO:0000045
    MAXO:0000046
    MAXO:0000047
    MAXO:0000048
    MAXO:0000050
    MAXO:0000051
    MAXO:0000054
    MAXO:0000055
    MAXO:0000056
    MAXO:0000067
    MAXO:0000071
    MAXO:0000075
    MAXO:0000092
    MAXO:0000093
    MAXO:0000096
    MAXO:0000097
    MAXO:0000123
    MAXO:0000131
    MAXO:0000132
    MAXO:0000162
    MAXO:0000172
    MAXO:0000175
    MAXO:0000179
    MAXO:0000207
    MAXO:0000211
    MAXO:0000219
    MAXO:0000235
    MAXO:0000236
    MAXO:0000245
    MAXO:0000255
    MAXO:0000257
    MAXO:0000258
    MAXO:0000264
    MAXO:0000268
    MAXO:0000270
    MAXO:0000271
    MAXO:0000275
    MAXO:0000276
    MAXO:0000277
    MAXO:0000279
    MAXO:0000280
    MAXO:0000281
    MAXO:0000282
    MAXO:0000284
    MAXO:0000286
    MAXO:0000288
    MAXO:0000289
    MAXO:0000291
    MAXO:0000298
    MAXO:0000304
    MAXO:0000306
    MAXO:0000308
    MAXO:0000309
    MAXO:0000314
    MAXO:0000317
    MAXO:0000318
    MAXO:0000319
    MAXO:0000320
    MAXO:0000321
    MAXO:0000441
    MAXO:0000442
    MAXO:0000457
    MAXO:0000465
    MAXO:0000477
    MAXO:0000614
    MAXO:0000644
    MAXO:0000654
    MAXO:0000659
    MAXO:0000664
    MAXO:0000684
    MAXO:0000723
    MAXO:0000846
    MAXO:0001003
    MAXO:0001004
    MAXO:0001009
    MAXO:0001124

  • Added new terms:
    MAXO_0000869 obstetric abdominal examination
    MAXO_0000870 pregnancy HCG test
    MAXO_0000871 obstetric cervical examination
    MAXO_0000872 cancer screening breast examination
    MAXO_0000873 hearing examination
    MAXO_0000874 albumin test for liver function
    MAXO_0000875 5'nucleotidase measurement for liver function
    MAXO_0000876 alkaline phosphatase measurement for liver function
    MAXO_0000877 calcium assessment for liver function
    MAXO_0000878 lactate dehydrogenase measurement for liver function
    MAXO_0000879 total bilirubin measurement for liver function
    MAXO_0000880 indirect bilirubin measurement for assessment of liver function

  • replaced MAXO_0000070 with MAXO_0001175 liver transplantation

  • replaced MAXO biopsy term with MAXO_0001175 biopsy

  • Added new OBI terms
    OBI_0002651 image guided biopsy
    OBI_0002652 computed tomography assisted biopsy
    OBI_0002653 ultrasound-guided needle biopsy
    OBI_0002654 needle biopsy
    OBI_0002655 fine needle aspiration biopsy
    OBI_0002656 core needle biopsy
    OBI_0002656 surgical biopsy

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March 2021 Release

22 Mar 20:48
@LCCarmody LCCarmody
v2021-03-22
cf3ee10
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March 2021 Release
  • Implemented an semi-automated ROBOT commands to update definitions taken from NCIT.
  • split the pharmacology pattern drug role vs. drug substance
  • updated logical definitions for the pharmacotherapy branch
  • set up new protein measurement patterns, including urine protein measurement, blood protein measurement, and serum protein measurement patterns
    New Terms:
    MAXO_0000865 protein measurement in blood
    MAXO_0001172 insulin measurement
    MAXO_0001173 albumin measurement in urine
    MAXO_0001174 serum protein measurement

updated terms
MAXO_0000605 protein measurement
MAXO_0000606 procalcitonin measurement
MAXO_0000607 D-dimer assessment
MAXO_0000833 thyroid-stimulating hormone test
MAXO_0000840 alanine transaminase test
MAXO_0000841 aspartate aminotransferase measurement
MAXO_0000842 gamma glutamyl transpeptidase measurement
MAXO_0000843 albumin measurement
MAXO_0000847 5' nuclotidase measurement
MAXO_0000854 haptoglobin measurement
MAXO_0000865 protein measurement in blood

merged MAXO_0000807 with MAXO_0000851 protein measurement in urine

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Second February 2021 release

24 Feb 20:50
@LCCarmody LCCarmody
2021-02-23
19703e9
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Second February 2021 release

The emphasis on this release was adding prenatal/fetal medical action terms, but there were additional terms added for structure or to correct mistakes. There were 2 new patterns added collection by location and examination by location. Terms are listed below

  • New terms
    MAXO_0000782 obstetrics and gynecology procedure
    MAXO_0000783 pregnancy test
    MAXO_0000784 HCG measurement
    MAXO_0000785 serum HCG measurement
    MAXO_0000786 urine HCG measurement
    MAXO_0000787 blood chemistry measurement
    MAXO_0000788 serum chemistry measurement
    MAXO_0000789 urine chemistry measurement
    MAXO_0000794 fundal height measurement
    MAXO_0000795 uterine size measurement
    MAXO_0000796 fetal heart rate monitoring
    MAXO_0000797 fetal Doppler measurement
    MAXO_0000798 internal fetal heart rate monitoring
    MAXO_0000799 pregnancy diet intake
    MAXO_0000800 avoid excessive heat
    MAXO_0000801 avoid toxoplasmosis exposure
    MAXO_0000802 avoid excessive exercise
    MAXO_0000803 avoid heavy lifting activities
    MAXO_0000804 avoid destabilizing activities
    MAXO_0000806 pregnancy education counseling
    MAXO_0000807 urine protein assessment
    MAXO_0000808 urine glucose measurement
    MAXO_0000809 syphilis screening
    MAXO_0000810 rubella antibody titer testing
    MAXO_0000811 varicella testing
    MAXO_0000812 hepatitis B assessment
    MAXO_0000813 hepatitis B surface antigen testing
    MAXO_0000814 HIV screening
    MAXO_0000815 chlamydia screening
    MAXO_0000816 gonorrhea testing
    MAXO_0000810 hepatitis C screening
    MAXO_0000821 blood typing procedure
    MAXO_0000822 ABO blood typing procedure
    MAXO_0000823 RH factor blood typing procedure
    MAXO_0000824 hemoglobin measurement
    MAXO_0000825 reticulocyte count
    MAXO_0000826 serum iron measurement
    MAXO_0000827 serum ferritin measurement
    MAXO_0000828 total iron capacity measurement
    MAXO_0000829 blood cell measurement
    MAXO_0000830 erythrocyte cell morphology measurement
    MAXO_0000831 blood smear test
    MAXO_0000832 serum creatinine measurement
    MAXO_0000833 thyroid-stimulating hormone test
    MAXO_0000834 T4 thyroid hormone test
    MAXO_0000835 T3 thyroid hormone test
    MAXO_0000836 blood coagulation test
    MAXO_0000837 partial thromboplastin time test
    MAXO_0000838 prothrombin time/international normalized ratio measurement
    MAXO_0000839 thrombin time measurement
    MAXO_0000840 alanine transaminase test
    MAXO_0000841 aspartate aminotransferase blood test
    MAXO_0000842 gamma glutamyl transferase measurement
    MAXO_0000843 albumin measurement
    MAXO_0000844 alkaline phosphatase measurement
    MAXO_0000845 total bilirubin measurement
    MAXO_0000846 lactate dehydrogenase measurement
    MAXO_0000847 5 prime nucleotidase measurement
    MAXO_0000848 bilirubin measurement
    MAXO_0000849 indirect bilirubin measurement
    MAXO_0000850 total protein measurement
    MAXO_0000851 urine protein measurement
    MAXO_0000852 24-hour urine collection
    MAXO_0000853 serum total protein measurement
    MAXO_0000854 haptoglobin protein measurement
    MAXO_0000855 hemoglobin electrophoresis test
    MAXO_0000856 serum PAPP-A measurement
    MAXO_0000858 glucose tolerance test
    MAXO_0000859 fetal examination
    MAXO_0000860 assessment of fetal presentation
    MAXO_0000861 labor induction
    MAXO_0000862 fetal Doppler velocimetry
    MAXO_0000863 fetal pulse oximetry
    MAXO_0001157 raw fish intake avoidance
    MAXO_0001158 unpasturized milk intake avoidance
    MAXO_0001159 endocervical swab collection
    MAXO_0001170 venous ultrasonography
    MAXO_0001171 testicular ultrasonography

  • examination by location pattern
    MAXO_0000790 clinical breast examination
    MAXO_0000791 breast self-examination
    MAXO_0000792 abdominal examination
    MAXO_0000793 pelvic examination
    MAXO_0001150 head examination
    MAXO_0001151 neck examination
    MAXO_0001152 chest examination
    MAXO_0001153 uterus examination
    MAXO_0001154 cervical examination
    MAXO_0001155 eye examination
    MAXO_0001156 whole body examination

  • collection by location pattern
    MAXO_0000819 blood specimen collection
    MAXO_0000820 bile specimen collection
    MAXO_0001160 sputum specimen collection
    MAXO_0001161 urine specimen collection
    MAXO_0001162 semen specimen collection
    MAXO_0001163 amniotic fluid specimen collection
    MAXO_0001164 pus specimen collection
    MAXO_0001165 mucus specimen collection
    MAXO_0001166 respiratory system mucus specimen collection
    MAXO_0001167 nasal mucus specimen collection
    MAXO_0001168 bodily fluid specimen collection
    MAXO_0001169 cerebrospinal fluid specimen collection

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February 2021 release

09 Feb 18:56
@LCCarmody LCCarmody
v2021-02-09
94d521c
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February 2021 release
  • ODK update
  • Change from Travis QC checks to GitHub actions
  • New term MAXO_0000780 human growth hormone replacement therapy was added
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Second December 2020 release

10 Dec 21:14
@LCCarmody LCCarmody
v2020-12-10
6a87905
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Second December 2020 release

Fixes 'abbreviation' annotation property to be specific for MAxO.

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December 2020 Release

07 Dec 19:41
@LCCarmody LCCarmody
v2020-12-07
3037e19
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December 2020 Release

  • Adjusted the nutrition intake hierarchy and added new terms
    -- MAXO_0000777 ferrous sulfate supplementation
    -- MAXO_0001149 magnesium supplementation
    -- MAXO_0000776 low FODMAP diet intake
    -- MAXO_0000775 exclusive formula feeding
    -- MAXO_0000766 low fat diet intake
    -- MAXO_0000767 prescriptive diet intake
    -- MAXO_0000767 small meal size recommendation
    -- MAXO_0000769 prescriptive vegetarian diet intake
    -- MAXO_0000770 carbohydrate controlled diet intake
    -- MAXO_0000771 carbohydrate restrictive diet intake
    -- MAXO_0000772 low purine diet intake
    -- MAXO_0000773 dash diet intake
    -- MAXO_0000762 parenteral nutrition intake
    -- MAXO_0000765 central venous nutrition intake
    -- MAXO_0000764 peripheral parenteral nutrition intake
    -- MAXO_0000763 partial parenteral nutrition intake

  • Added new supplementation terms
    -- MAXO:0000760 vitamin b12 supplementation
    -- MAXO:0000761 vitamin b supplementation
    -- MAXO:0001128 folic acid supplementation
    -- MAXO:0001129 vitamin supplementation
    -- MAXO:0001130 nicotinic acid supplementation
    -- MAXO:0001131 pyridoxine supplementation
    -- MAXO:0001133 ascorbic acid supplementation
    -- MAXO:0001134 sodium pyruvate supplementation
    -- MAXO:0001135 fat-soluble vitamin supplementation
    -- MAXO:0001136 S-adenosyl methionine supplementation
    -- MAXO:0001137 isoleucine supplementation
    -- MAXO:0001138 valine supplementation
    -- MAXO:0001139 calcium supplementation
    -- MAXO:0001140 calcium carbonate supplementation
    -- MAXO:0001141 glucose supplementation
    -- MAXO:0001142 docosahexaenoic acid supplementation
    -- MAXO:0001143 omega-3 fatty acid supplementation
    -- MAXO:0001144 lutein supplementation
    -- MAXO:0001145 ribose supplementation
    -- MAXO:0001146 fluoride supplementation
    -- MAXO:0001147 soluble fiber supplementation
    -- MAXO:0001148 fish oil supplementation

  • replace MAXO:0030012 obsolete phenylalanine restricted diet intake with MAXO:0010094 phenylalanine restricted diet intake

  • Added new terms related to Fanconi Anemia
    -- MAXO_0000745 cytogenetic analysis
    -- MAXO_0000747 hematopoietic stem cell transplantation
    -- MAXO_0000749 T cell-depleted hematopoietic stem cell transplantation
    -- MAXO_0000759 HPV vaccination
    -- MAXO_0000750 transplant conditioning
    -- MAXO_0000750 clinical surveilance
    -- MAXO_0000753 bone marrow examination
    -- MAXO_0000752 bone marrow aspiration
    -- MAXO_0000754 cellularity measurement
    -- MAXO_0000755 liquid biopsy
    -- MAXO_0001126avoid blood transfusion
    -- MAXO_0000758 avoid unprotected sexual intercourse
    -- MAXO_0000746 chromosomal breakage analysis

  • Terms added for pharmacotherapy usage
    -- MAXO_0000744 menopausal hormone therapy
    -- MAXO_0000652 ACE inhibitory therapy
    -- MAXO_0000655 ACE 1 inhibitor therapy
    -- MAXO_0000656 ACE 2 inhibitor therapy
    -- MAXO_0000738 bile acid sequestrant therapy
    -- MAXO_0000737 fibrate antilipedemic agent therapy
    -- MAXO_0000739 HMG-CoA reductase inhibitor therapy
    -- MAXO_0000740 nicotinic acid agent therapy (niacin therapy)
    -- MAXO_0001123 potassium supplementation
    -- MAXO_0000741 potassium-sparing diuretic agent therapy
    -- MAXO_0001125 loop diuretic agent therapy
    -- MAXO_0000743 sulfonylurea agent therapy
    -- MAXO_0000164 uricosuric agent therapy
    -- MAXO_0000742 thiazide diuretic agent therapy

  • Other term added
    -- MAXO_0000748
    fecal microbiota transplantation

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November 2020 Release

16 Nov 18:34
@LCCarmody LCCarmody
v2020-11-16
1d694ca
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November 2020 Release

  • Update 'avoid_phenotype' pattern to deal with capitalization issue with HP.

  • Update label and synonyms for 'testing, screening, examination, and assessment' to make sure that they are consistent throughout MAxO.

  • Obsolete: MAXO_0001112 was obsolete because inadvertently kidney ct and biopsy of the kidney both pointed to the same MAXO ID. New terms have been created.

  • Imported OBI and incorporated 'collecting specimen with swab'OBI_0002600.

  • Begun adding 'Allied health professional examination terms', but the branch still needs more work.

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