LOAD THEME CONVERSION SHORTCUTS

  source theme-aliases

IDENTIFIER CONVERSION

  {Chem|Disz|Gene|Mesh}{Code|Desc|Name|Tree}To{Code|Desc|Name|Tree}

THEME-BASED NAVIGATION

  {Chem|Disz|Gene}To{Chem|Disz|Gene}

THEME EXAMPLES

  ChemNameToCode dapsone

  echo dapsone | ChemNameToCode

  echo "familial mediterranean fever" |
  DiszNameToCode |
  DiszToGene |
  GeneToDisz |
  DiszToChem |
  ChemCodeToName |
  sort -f | uniq -i

  echo "sarcoidosis" |
  DiszNameToCode |
  DiszToChem |
  ChemToDisz |
  DiszToChem |
  ChemCodeToName |
  sort -f | uniq -i

  echo "wilms tumor" |
  DiszNameToCode |
  DiszToGene |
  GeneToGene |
  GeneToChem |
  ChemCodeToName |
  sort -f | uniq -i

AUTOMATION

  ascend_mesh_tree() {
    var="${1%\*}"
    target=""
    ev=$( rchive -local pubmed )
    if [ -n "$ev" ]
    then
      # only care about master volume and its Data subfolder
      target="${ev%:*}"
      target=${target%/}
    fi
    while :
    do
      frst=$( phrase-search -count "$var* [TREE]" )
      scnd=$( cat "${target}/Data/meshconv.xml" |
              xtract -pattern Rec -if Tree -equals "$var" -first Code Name )
      printf "${frst}\t${scnd}\n"
      case "$var" in
        *.* ) var="${var%????}" ;;
        *   ) break             ;;
      esac
    done |
    align-columns -g 4
  }

  ascend_mesh_tree "C01.925.782.417.415"


  for thm in A+ A- B C D E E+ E- G H I J K L Md Mp N O Pa Pr Q Rg Sa T Te U Ud V+ W X Y Z
  do
    num=$(phrase-search -query "$thm [THME]" | wc -l)
    echo -e "$thm\t$num"
  done


  declare -a THEMES
  THEMES=( A+ A- B Bc Bg C D E E+ E- Ec Ec+ Ec- \
           Eg Eg+ G H I J Jc Jg K L Md Mp N O Pa \
           Pr Q Rg Sa T Te U Ud V+ W X Y Z )
  declare -a REMAINS
  REMAINS=("${THEMES[@]:1}")

  for fst in ${THEMES[@]}
  do
    num=$(phrase-search -query "$fst [THME]" | wc -l)
    echo -e "$fst\t \t$num"
    for scd in ${REMAINS[@]}
    do
      num=$(phrase-search -query "$fst [THME] AND $scd [THME]" | wc -l)
      echo -e "$fst\t$scd\t$num"
      echo -e "$scd\t$fst\t$num"
    done
    REMAINS=("${REMAINS[@]:1}")
  done | sort | expand -t 7,13


  cat meshconv.xml |
  xtract -pattern Rec -if "%Tree" -eq 3 -sep " - " -tab "\n" -element Tree,Name |
  sort

ENTREZ INTEGRATION

  esearch -db pubmed -query "complement system proteins [MESH]" |
  efetch -format uid |
  phrase-search -filter "L [THME] AND D10* [TREE]"

MEDICAL SUBJECT HEADING CODE VIEWERS

  https://meshb.nlm.nih.gov/treeView
  https://meshb-prev.nlm.nih.gov/treeView

MESH CATEGORIES IN TREE INDEX

  A - Anatomy
  C - Diseases
  D - Chemicals and Drugs
  E - Analytical, Diagnostic and Therapeutic Techniques, and Equipment
  F - Psychiatry and Psychology
  G - Phenomena and Processes
  Z - Geographicals

UNINDEXED MESH CATEGORIES

  B - Organisms
  H - Disciplines and Occupations
  I - Anthropology, Education, Sociology, and Social Phenomena
  J - Technology, Industry, and Agriculture
  K - Humanities
  L - Information Science
  M - Named Groups
  N - Health Care
  V - Publication Characteristics

INDEXED MESH CODES

  A01 - Body Regions
  A02 - Musculoskeletal System
  A03 - Digestive System
  A04 - Respiratory System
  A05 - Urogenital System
  A06 - Endocrine System
  A07 - Cardiovascular System
  A08 - Nervous System
  A09 - Sense Organs
  A10 - Tissues
  A11 - Cells
  A12 - Fluids and Secretions
  A13 - Animal Structures
  A14 - Stomatognathic System
  A15 - Hemic and Immune Systems
  A16 - Embryonic Structures
  A17 - Integumentary System
  A18 - Plant Structures
  A19 - Fungal Structures
  A20 - Bacterial Structures
  A21 - Viral Structures

  C01 - Infections
  C04 - Neoplasms
  C05 - Musculoskeletal Diseases
  C06 - Digestive System Diseases
  C07 - Stomatognathic Diseases
  C08 - Respiratory Tract Diseases
  C09 - Otorhinolaryngologic Diseases
  C10 - Nervous System Diseases
  C11 - Eye Diseases
  C12 - Male Urogenital Diseases
  C13 - Female Urogenital Diseases and Pregnancy Complications
  C14 - Cardiovascular Diseases
  C15 - Hemic and Lymphatic Diseases
  C16 - Congenital, Hereditary, and Neonatal Diseases and Abnormalities
  C17 - Skin and Connective Tissue Diseases
  C18 - Nutritional and Metabolic Diseases
  C19 - Endocrine System Diseases
  C20 - Immune System Diseases
  C21 - Disorders of Environmental Origin
  C22 - Animal Diseases
  C23 - Pathological Conditions, Signs and Symptoms
  C24 - Occupational Diseases
  C25 - Chemically-Induced Disorders
  C26 - Wounds and Injuries

  D01 - Inorganic Chemicals
  D02 - Organic Chemicals
  D03 - Heterocyclic Compounds
  D04 - Polycyclic Compounds
  D05 - Macromolecular Substances
  D08 - Enzymes and Coenzymes
  D09 - Carbohydrates
  D10 - Lipids
  D12 - Amino Acids, Peptides, and Proteins
  D13 - Nucleic Acids, Nucleotides, and Nucleosides
  D20 - Complex Mixtures
  D23 - Biological Factors
  D26 - Pharmaceutical Preparations
  D27 - Chemical Actions and Uses

  E01 - Diagnosis
  E02 - Therapeutics
  E03 - Anesthesia and Analgesia
  E04 - Surgical Procedures, Operative
  E05 - Investigative Techniques
  E07 - Equipment and Supplies

  F01 - Behavior and Behavior Mechanisms
  F02 - Psychological Phenomena
  F03 - Mental Disorders
  F04 - Behavioral Disciplines and Activities

  G01 - Physical Phenomena
  G02 - Chemical Phenomena
  G03 - Metabolism
  G04 - Cell Physiological Phenomena
  G05 - Genetic Phenomena
  G06 - Microbiological Phenomena
  G07 - Physiological Phenomena
  G08 - Reproductive and Urinary Physiological Phenomena
  G09 - Circulatory and Respiratory Physiological Phenomena
  G10 - Digestive System and Oral Physiological Phenomena
  G11 - Musculoskeletal and Neural Physiological Phenomena
  G12 - Immune System Phenomena
  G13 - Integumentary System Physiological Phenomena
  G14 - Ocular Physiological Phenomena
  G15 - Plant Physiological Phenomena
  G16 - Biological Phenomena
  G17 - Mathematical Concepts

  Z01 - Geographic Locations

MESH SUBHEADINGS

  abnormalities
  administration & dosage
  adverse effects
  agonists
  analogs & derivatives
  analysis
  anatomy & histology
  antagonists & inhibitors
  biosynthesis
  blood
  blood supply
  cerebrospinal fluid
  chemical synthesis
  chemically induced
  chemistry
  classification
  complications
  congenital
  cytology
  deficiency
  diagnosis
  diagnostic imaging
  diet therapy
  drug effects
  drug therapy
  economics
  education
  embryology
  enzymology
  epidemiology
  ethics
  ethnology
  etiology
  genetics
  growth & development
  history
  immunology
  injuries
  innervation
  instrumentation
  isolation & purification
  legislation & jurisprudence
  manpower
  metabolism
  methods
  microbiology
  mortality
  nursing
  organization & administration
  parasitology
  pathogenicity
  pathology
  pharmacokinetics
  pharmacology
  physiology
  physiopathology
  poisoning
  prevention & control
  psychology
  radiation effects
  radiotherapy
  rehabilitation
  secondary
  secretion
  standards
  statistics & numerical data
  supply & distribution
  surgery
  therapeutic use
  therapy
  toxicity
  transmission
  transplantation
  trends
  ultrastructure
  urine
  utilization
  veterinary
  virology

THEME CODES:

Chemical-Gene

  A+    agonism, activation
  A-    antagonism, blocking
  Bc    binding, ligand (especially receptors)
  Ec+   increases expression/production
  Ec-   decreases expression/production
  Ec    affects expression/production (neutral)
  N     inhibits

Gene-Chemical

  O     transport, channels
  K     metabolism, pharmacokinetics
  Z     enzyme activity

Chemical-Disease

  T     treatment/therapy (including investigatory)
  C     inhibits cell growth (especially cancers)
  Sa    side effect/adverse event
  Pr    prevents, suppresses
  Pa    alleviates, reduces
  Jc    role in disease pathogenesis

Disease-Chemical

  Mp    biomarkers (of disease progression)

Gene-Disease

  U     causal mutations
  Ud    mutations affecting disease course
  D     drug targets
  Jg    role in pathogenesis
  Te    possible therapeutic effect
  Y     polymorphisms alter risk
  G     promotes progression

Disease-Gene

  Md    biomarkers (diagnostic)
  X     overexpression in disease
  L     improper regulation linked to disease

Gene-Gene

  Bg    binding, ligand (especially receptors)
  W     enhances response
  V+    activates, stimulates
  Eg+   increases expression/production
  Eg    affects expression/production (neutral)
  I     signaling pathway
  H     same protein or complex
  Rg    regulation
  Q     production by cell population

THEME TABLE:

  A+    Agonism, activation                      N     Inhibits
  A-    Antagonism, blocking                     O     Transport, channels
  B     Binding, ligand                          Pa    Alleviates, reduces
  C     Inhibits cell growth                     Pr    Prevents, suppresses
  D     Drug targets                             Q     Production by cell population
  E     Affects expression/production            Rg    Regulation
  E+    Increases expression/production          Sa    Side effect/adverse event
  E-    Decreases expression/production          T     Treatment/therapy
  G     Promotes progression                     Te    Possible therapeutic effect
  H     Same protein or complex                  U     Causal mutations
  I     Signaling pathway                        Ud    Mutations affecting disease course
  J     Role in disease pathogenesis             V+    Activates, stimulates
  K     Metabolism, pharmacokinetics             W     Enhances response
  L     Improper regulation linked to disease    X     Overexpression in disease
  Md    Biomarkers (diagnostic)                  Y     Polymorphisms alter risk
  Mp    Biomarkers (progression)                 Z     Enzyme activity
