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Build out MIC extraction template #495

Merged
merged 21 commits into from
Dec 20, 2024
Merged

Build out MIC extraction template #495

merged 21 commits into from
Dec 20, 2024

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caufieldjh
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@caufieldjh caufieldjh commented Dec 18, 2024 •
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Template for extraction from the Micronutrient Information Center (https://lpi.oregonstate.edu/mic)

@caufieldjh caufieldjh linked an issue Dec 18, 2024 that may be closed by this pull request
Expand micronutrient.yaml to support Disease, Phenotype, Biological Process, Food Associations #492
Closed
@caufieldjh
Class name change; descriptions
c5aa925
@caufieldjh
Minor class name tweak
3d375cf
@caufieldjh
Add nutrient vs nutrient relationships
91383a1
@caufieldjh
Add nutrient to phenotype relationships
7b7e5ad
@caufieldjh
prompt tuning
c10af08
@caufieldjh
More prompt tuning for phenotypes
99cdb0f
@caufieldjh
Add NutrientToBiologicalProcessRelationship
e31787e
@caufieldjh
Minor prompt tuning
fcf2104
@caufieldjh
Add NutrientToHealthStatusRelationship
3c3c0ab
@caufieldjh
small fix for NutrientToBiologicalProcessRelationship
dfccd69
@caufieldjh
Tuning for nutrient_to_nutrient_relationships
5ebc50c
@caufieldjh
Tuning for nutrient_to_biological_process_relationships
96b8f44
@caufieldjh
Add NutrientToSourceRelationship
096fc3b
@caufieldjh
Comment out redundant nutrient_terms slot
295080f
@caufieldjh
First pass at reference extraction
faacb2e
@caufieldjh
Second pass at reference extraction
4ba63a2
@caufieldjh
Extracting full reflist isn't working. Commenting out
54a65ba
@caufieldjh
Tuning reference extraction
508f826
@caufieldjh
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This extracts reference numbers too, though in testing I could not get the refs to be cleanly linked to individual references without modifications to details (e.g., publication years getting changed).
So that may be a job for more traditional scraping since the reference numbers refer to the References section on each page.

Example (w/ Llama 3.3 70B on LBL CBORG):

$ ontogpt -vvv web-extract -t mic -m lbl/cborg-chat:latest --model-provider openai --api-base "https://api.cborg.lbl.gov" https://lpi.oregonstate.edu/mic/minerals/magnesium -o mic_check.yaml

extracted_object:
  id: 5de2d86d-0fd8-44f4-aad3-a8dfd59a39f0
  label: Magnesium
  nutrient_to_disease_relationships:
    - references:
        - '15'
        - '16'
        - '17'
        - '18'
      nutrient: CHEBI:25107
      relationship: DECREASES RISK OF
      disease: MONDO:0000816
    - references:
        - '26'
        - '41'
        - '42'
        - '43'
      nutrient: CHEBI:25107
      relationship: DECREASES RISK OF
      disease: MONDO:0004995
    - references:
        - '62'
        - '63'
        - '64'
        - '65'
        - '66'
      nutrient: CHEBI:25107
      relationship: DECREASES RISK OF
      disease: MONDO:0005015
    - references:
        - '77'
        - '78'
        - '79'
        - '80'
        - '81'
      nutrient: CHEBI:25107
      relationship: DECREASES RISK OF
      disease: MONDO:0005298
    - references:
        - '96'
        - '97'
        - '98'
        - '99'
        - '100'
      nutrient: CHEBI:25107
      relationship: TREATS
      disease: MONDO:0024575
    - references:
        - '110'
        - '111'
        - '112'
        - '113'
      nutrient: CHEBI:25107
      relationship: TREATS
      disease: MONDO:0004995
    - references:
        - '133'
        - '134'
        - '135'
      nutrient: CHEBI:25107
      relationship: TREATS
      disease: MONDO:0005015
    - references:
        - '136'
        - '137'
        - '138'
        - '139'
        - '140'
      nutrient: CHEBI:25107
      relationship: TREATS
      disease: MONDO:0100470
    - references:
        - '144'
        - '145'
        - '146'
        - '147'
        - '148'
      nutrient: CHEBI:25107
      relationship: TREATS
      disease: Pain management
    - references:
        - '162'
        - '163'
        - '164'
        - '165'
        - '166'
      nutrient: CHEBI:25107
      relationship: TREATS
      disease: Migraine headaches
    - references:
        - '175'
        - '176'
        - '177'
        - '178'
      nutrient: CHEBI:25107
      relationship: TREATS
      disease: Critical injury or illness
  nutrient_to_phenotype_relationships:
    - references:
        - '65'
        - '68'
        - '69'
        - '70'
        - '71'
      nutrient: CHEBI:25107
      relationship: IMPROVES
      phenotype: Insulin sensitivity
    - references:
        - '20'
        - '21'
      nutrient: CHEBI:25107
      relationship: REDUCES
      phenotype: Systemic inflammation
    - references:
        - '77'
        - '78'
        - '79'
        - '80'
        - '81'
      nutrient: CHEBI:25107
      relationship: IMPROVES
      phenotype: Bone mineral density
    - references:
        - '87'
        - '88'
        - '89'
        - '90'
        - '91'
      nutrient: CHEBI:25107
      relationship: IMPROVES
      phenotype: Muscle strength
    - references:
        - '144'
        - '145'
        - '146'
        - '147'
        - '148'
      nutrient: CHEBI:25107
      relationship: REDUCES
      phenotype: HP:0012531
    - references:
        - '162'
        - '163'
        - '164'
        - '165'
        - '166'
      nutrient: CHEBI:25107
      relationship: REDUCES
      phenotype: Migraine headache frequency
  nutrient_to_biological_process_relationships:
    - references:
        - '2'
        - '3'
      nutrient: CHEBI:25107
      relationship: REGULATES
      process: Energy production
    - references:
        - '2'
        - '3'
      nutrient: CHEBI:25107
      relationship: REGULATES
      process: Synthesis of essential molecules
    - references:
        - '2'
        - '3'
      nutrient: CHEBI:25107
      relationship: REGULATES
      process: Ion transport across cell membranes
    - references:
        - '2'
        - '3'
      nutrient: CHEBI:25107
      relationship: REGULATES
      process: Cell signaling
    - references:
        - '2'
        - '3'
      nutrient: CHEBI:25107
      relationship: REGULATES
      process: GO:0016477
    - references:
        - '4'
      nutrient: CHEBI:25107
      relationship: INTERACTS WITH
      process: Zinc
    - references:
        - '2'
        - '3'
      nutrient: CHEBI:25107
      relationship: INTERACTS WITH
      process: Fiber
    - references:
        - '5'
      nutrient: CHEBI:25107
      relationship: INTERACTS WITH
      process: Protein
    - references:
        - '6'
      nutrient: CHEBI:25107
      relationship: INTERACTS WITH
      process: Vitamin D and calcium
  nutrient_to_health_status_relationships:
    - references:
        - '77'
        - '78'
        - '79'
        - '80'
        - '81'
      nutrient: CHEBI:25107
      relationship: SUPPORTS HEALTH OF
      anatomy: UBERON:0001434
    - references:
        - '26'
        - '41'
        - '42'
        - '43'
      nutrient: CHEBI:25107
      relationship: SUPPORTS HEALTH OF
      anatomy: UBERON:0004535
    - references:
        - '144'
        - '145'
        - '146'
        - '147'
        - '148'
      nutrient: CHEBI:25107
      relationship: SUPPORTS HEALTH OF
      anatomy: UBERON:0001016
    - references:
        - '87'
        - '88'
        - '89'
        - '90'
        - '91'
      nutrient: CHEBI:25107
      relationship: SUPPORTS HEALTH OF
      anatomy: UBERON:0000383
  nutrient_to_source_relationships:
    - references:
        - '2'
      nutrient: CHEBI:25107
      relationship: PROVIDED BY
      source: Green leafy vegetables
    - references:
        - '2'
      nutrient: CHEBI:25107
      relationship: PROVIDED BY
      source: Unrefined grains
    - references:
        - '2'
      nutrient: CHEBI:25107
      relationship: PROVIDED BY
      source: FOODON:03303171
    - references:
        - '2'
      nutrient: CHEBI:25107
      relationship: PROVIDED BY
      source: FOODON:03310646
    - references:
        - '2'
      nutrient: CHEBI:25107
      relationship: PROVIDED BY
      source: FOODON:03411222
    - references:
        - '2'
      nutrient: CHEBI:25107
      relationship: PROVIDED BY
      source: FOODON:00001256
    - references:
        - '180'
        - '181'
        - '182'
      nutrient: CHEBI:25107
      relationship: PROVIDED BY
      source: Supplements
  nutrient_to_nutrient_relationships:
    - references:
        - '4'
      nutrient_subject: CHEBI:25107
      relationship: INTERACTS WITH
      nutrient_object: CHEBI:27363
    - references:
        - '2'
        - '3'
      nutrient_subject: CHEBI:25107
      relationship: INTERACTS WITH
      nutrient_object: Fiber
    - references:
        - '5'
      nutrient_subject: CHEBI:25107
      relationship: INTERACTS WITH
      nutrient_object: CHEBI:36080
    - references:
        - '6'
      nutrient_subject: CHEBI:25107
      relationship: INTERACTS WITH
      nutrient_object: CHEBI:22984
named_entities:
  - id: CHEBI:25107
    label: Magnesium
    original_spans:
      - 43:51
      - 682:690
      - 1920:1928
      - 2880:2888
      - 2921:2929
      - 3211:3219
      - 3646:3654
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      - 8524:8532
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      - 8943:8951
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  - id: MONDO:0000816
    label: Metabolic syndrome
    original_spans:
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  - id: MONDO:0004995
    label: Cardiovascular disease
    original_spans:
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  - id: MONDO:0005015
    label: Diabetes mellitus
    original_spans:
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      - 3421:3437
      - 4445:4461
      - 4573:4589
      - 5226:5242
      - 10327:10343
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      - 52414:52430
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      - 53512:53528
      - 85815:85831
  - id: MONDO:0005298
    label: Osteoporosis
    original_spans:
      - 3324:3335
      - 4351:4362
      - 33773:33784
      - 33860:33871
      - 34484:34495
      - 34921:34932
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      - 87834:87845
      - 88110:88121
      - 88279:88290
      - 88468:88479
      - 89841:89852
  - id: MONDO:0024575
    label: Pregnancy complications
    original_spans:
      - 3372:3394
      - 39196:39218
  - id: MONDO:0100470
    label: Asthma
    original_spans:
      - 3440:3445
      - 5245:5250
      - 54021:54026
      - 54095:54100
      - 54130:54135
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      - 54404:54409
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  - id: HP:0012531
    label: Pain
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      - 3448:3451
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      - 56069:56072
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  - id: GO:0016477
    label: Cell migration
    original_spans:
      - 3113:3126
      - 7976:7989
      - 8134:8147
  - id: UBERON:0001434
    label: Skeletal system
  - id: UBERON:0004535
    label: Cardiovascular system
  - id: UBERON:0001016
    label: Nervous system
    original_spans:
      - 102611:102624
  - id: UBERON:0000383
    label: Muscular system
  - id: FOODON:03303171
    label: Nuts
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      - 65997:66000
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      - 71032:71035
  - id: FOODON:03310646
    label: Legumes
    original_spans:
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      - 5482:5488
  - id: FOODON:03411222
    label: Fish
    original_spans:
      - 65535:65538
  - id: FOODON:00001256
    label: Dairy products
  - id: CHEBI:27363
    label: Zinc
    original_spans:
      - 761:764
      - 1999:2002
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      - 8233:8236
      - 8338:8341
      - 8436:8439
      - 73000:73003
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  - id: CHEBI:36080
    label: Protein
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      - 39609:39615
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  - id: CHEBI:22984
    label: calcium
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      - 80375:80381
      - 89122:89128
      - 89981:89987
      - 106850:106856
      - 110153:110159
      - 111930:111936

@caufieldjh caufieldjh marked this pull request as ready for review December 20, 2024 18:29
@caufieldjh caufieldjh merged commit 1284863 into main Dec 20, 2024
4 checks passed
@caufieldjh caufieldjh deleted the 492-expand-micronutrientyaml-to-support-disease-phenotype-biological-process-food-associations branch December 20, 2024 18:30
@kevinschaper kevinschaper mentioned this pull request Dec 20, 2024
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Expand micronutrient.yaml to support Disease, Phenotype, Biological Process, Food Associations
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@caufieldjh