1 Line of Code to Use 200+ State-of-the-Art Clinical & Biomedical NLP Models - Webinar Sept 16 2021¶
In this notebook we will cover almost every feature, model and domain solutions provided by NLU healthcare! This is a birds eye overview and crash course of almost everything you can do with a healthcare license and NLU!
All Healthcare Models and Domains provided by JSL overview¶
NER Domains and Models Overview¶
Named entities are sub-strings in a text that can be classified into catogires of a domain. For example, in the String
"Tesla is a great stock to invest in " , the sub-string "Tesla" is a named entity, it can be classified with the label company by an ML algorithm.
Named entities can easily be extracted by the various pre-trained Deep Learning based NER algorithms provided by NLU.
NER models can be trained for many different domains and aquire expert domain knowledge in each of them. JSL provides a wide array of experts for various Medical, Helathcare and Clinical domains
This algorithm is provided by Spark NLP for Healthcare's MedicalNerModel
| Domain | Description | Sample NLU Spells | Sample Entities | Sample Predicted Labels | Reference Links |
|---|---|---|---|---|---|
| ADE (Adverse Drug Events) | Find adverse drug event (ADE) related entities | med_ner.ade_biobert |
Aspirin , vomiting |
DRUG, ADE |
CADEC, Twimed |
| Anatomy | Find body parts, anatomical sites a nd reference related entities | med_ner.anatomy |
tubules, nasopharyngeal aspirates, embryoid bodies, NK cells, Mitochondrial, tracheoesophageal fistulas, heart, colon cancer, cervical, central nervous system |
Tissue_structure, Organism_substance, Developing_anatomical_structure, Cell, Cellular_component, Immaterial_anatomical_entity, organ, Pathological_formation, Organism_subdivision, Anatomical_system |
AnEM |
| Cellular/Molecular Biology | Find Genes, Molecules, Cell or general Biology related entities | med_ner.cellular.biobert |
human T-cell leukemia virus type 1 Tax-responsive , primary T lymphocytes, E1A-immortalized, Spi-B mRNA, zeta-globin |
DNA, Cell_type, Cell_line, RNA, Protein |
JNLPBA |
| Chemical/Genes/Proteins | Find Chemical, Gene and Protein related entities | med_ner.chemprot.clinical |
nitrogen , β-amyloid , NF-kappaB |
CHEMICAL, GENE-Y, GENE-N |
ChemProt |
| Chemical Compounds | Find general chemical compound related entities | med_ner.chemicals |
resveratrol , β-polyphenol |
CHEM |
Dataset by John Snow Labs |
| Drug Chemicals | Find chemical and drug related entities | med_ner.drugs |
potassium , anthracyclines, taxanes |
DrugChem.DrugChem.DrugChem |
i2b2 + FDA |
| Posology/Drugs | Find posology and drug related entities | med_ner.posology.biobert |
5000 units, Aspirin, 14 days, tablets, daily, topically, 30 mg |
DOSAGE, DRUG, DURATION, FORM, FREQUENCY, ROUTE, STRENGTH. |
i2b2 + FDA |
| Risk Factors | Find risk factor of patient related entities | med_ner.risk_factors.biobert |
coronary artery disease, hypertension, Smokes 2 packs of cigarettes per day, morbid obesity, Actos, Works in School, diabetic, diabetic |
CAD, HYPERTENSION, SMOKER, OBESE, FAMILY_HIST, MEDICATION, PHI, HYPERLIPIDEMIA, DIABETES |
De-identification and Heart Disease Risk Factors Challenge datasets |
| cancer Genetics | Find cancer and genetics related entities | med_ner.cancer |
human, Kir 3.3, GIRK3, potassium, GIRK, chromosome 1q21-23, pancreas, tissues, fat andskeletal muscle, KCNJ9, Type II, breast cancer, patients, anthracyclines, taxanes, vinorelbine, patients, breast, vinorelbine inpatients, anthracyclines |
Amino_acid, Anatomical_system, cancer, Cell, Cellular_component, Developing_anatomical_Structure , Gene_or_gene_product, Immaterial_anatomical_entity, Multi-tissue_structure, Organ, Organism , Organism_subdivision, Simple_chemical, Tissue |
CG TASK of BioNLP 2013 |
| Diseases | Find disease related entities | med_ner.diseases.biobert |
the cyst, a large Prolene suture, a very small incisional hernia, the hernia cavity, omentum, the hernia, the wound lesion, The lesion, the existing scar, the cyst, the wound, this cyst down to its base, a small incisional hernia, The cyst |
Disease |
CG TASK of BioNLP 2013 |
| Bacterial Species | Find bacterial species related entities | med_ner.bacterial_species |
Neisseria wadsworthii, N. bacilliformis, Spirochaeta litoralis |
SPECIES |
Dataset by John Snow Labs |
| Medical Problem/Test/Treatment | Find medical problem,test and treatment related entities | med_ner.healthcare |
respiratory tract infection , Ourexpression studies, atorvastatin |
PROBLEM, TEST, TREATMENT |
i2b2 |
| Clinical Admission Events | Find clinical admission event related entities | med_ner.admission_events |
2007, 12 AM, Headache, blood sample, presented, emergency room, daily |
DATE, TIME, PROBLEM, TEST, TREATMENT, OCCURENCE, CLINICAL_DEPT, EVIDENTIAL, DURATION, FREQUENCY, ADMISSION, DISCHARGE |
Custom i2b2, enriched with Events |
| Genetic Variants | Find genetic variant related entities | en.med_ner.genetic_variants |
rs1061170, p.S45P, T13046C |
DNAMutation, ProteinMutation, SNP |
TMVAR |
| PHI (Protected Healthcare Information) | Find PHI(Protected Healthcare) related entities | en.med_ner.deid |
2093-01-13, David Hale, Hendrickson,</br> Ora, 7194334, 01/13/93, Oliveira, 25-year-old, 1-11-2000, Cocke County Baptist Hospital, 0295 Keats Street., (302) 786-5227, Brothers Coal-Mine |
MEDICALRECORD, ORGANIZATION, DOCTOR, USERNAME, PROFESSION, HEALTHPLAN, URL, CITY, DATE, LOCATION-OTHER, STATE, PATIENT, DEVICE, COUNTRY, ZIP, PHONE, HOSPITAL, EMAIL, IDNUM, SREET, BIOID, FAX, AGE |
n2c2 i2b2-PHI |
| Social Determinants / Demographic Data | Find Social Determinants and Demographic Data Related Entities | med_ner.jsl.enriched |
21-day-old, male, congestion, mom, suctioning yellow discharge, she, problems with his breathing, perioral cyanosis, retractions, mom, Tylenol, His, his, respiratory congestion, He, tired, fussy, albuterol |
Age, Diagnosis, Dosage, Drug_Name, Frequency, Gender, Lab_Name, Lab_Result, Symptom_Name |
Dataset by John Snow Labs |
| General Clinical | Find General Clinical Entities | med_ner.jsl.wip.clinical.modifier |
28-year-old, female, gestational, diabetes, mellitus, eight, years, prior, type, two, diabetes, mellitus, T2DM, HTG-induced, pancreatitis, three, years, prior, acute, hepatitis, obesity, body, mass, index, BMI, kg/m2, polyuria, polydipsia, poor, appetite, vomiting, Two, weeks, prior, she, five-day, course |
Injury_or_Poisoning, Direction, Test, Admission_Discharge, Death_Entity, Relationship_Status, Duration, Respiration, Hyperlipidemia, Birth_Entity, Age, Labour_Delivery, Family_History_Header, BMI, Temperature, Alcohol, Kidney_Disease, Oncological, Medical_History_Header, Cerebrovascular_Disease, Oxygen_Therapy, O2_Saturation, Psychological_Condition, Heart_Disease, Employment, Obesity, Disease_Syndrome_Disorder, Pregnancy, ImagingFindings, Procedure, Medical_Device, Race_Ethnicity, Section_Header, Symptom, Treatment, Substance, Route, Drug_Ingredient, Blood_Pressure, Diet, External_body_part_or_region, LDL, VS_Finding, Allergen, EKG_Findings, Imaging_Technique, Triglycerides, RelativeTime, Gender, Pulse, Social_History_Header, Substance_Quantity, Diabetes, Modifier, Internal_organ_or_component, Clinical_Dept, Form, Drug_BrandName, Strength, Fetus_NewBorn, RelativeDate, Height, Test_Result, Sexually_Active_or_Sexual_Orientation, Frequency, Time, Weight, Vaccine, Vital_Signs_Header, Communicable_Disease, Dosage, Overweight, Hypertension, HDL, Total_Cholesterol, Smoking, ` |
Dataset by John Snow Labs |
| Radiology | Find Radiology related entities | med_ner.radiology.wip_clinical |
Bilateral, breast, ultrasound, ovoid mass, 0.5 x 0.5 x 0.4, cm, anteromedial aspect, left, shoulder, mass, isoechoic echotexture, muscle, internal color flow, benign fibrous tissue, lipoma |
ImagingTest, Imaging_Technique, ImagingFindings, OtherFindings, BodyPart, Direction, Test, Symptom, Disease_Syndrome_Disorder, Medical_Device, Procedure, Measurements, Units |
Dataset by John Snow Labs, MIMIC-CXR and MT Radiology texts |
| Radiology Clinical JSL-V1 | Find radiology related entities in clinical setting | med_ner.radiology.wip_greedy_biobert |
Bilateral, breast, ultrasound, ovoid mass, 0.5 x 0.5 x 0.4, cm, anteromedial aspect, left, shoulder, mass, isoechoic echotexture, muscle, internal color flow, benign fibrous tissue, lipoma |
Test_Result, OtherFindings, BodyPart, ImagingFindings, Disease_Syndrome_Disorder, ImagingTest, Measurements, Procedure, Score, Test, Medical_Device, Direction, Symptom, Imaging_Technique, ManualFix, Units |
Dataset by John Snow Labs, |
| Genes and Phenotypes | Find Genes and Phenotypes (the observable physical properties of an organism) related entities | med_ner.human_phenotype.gene_biobert |
APOC4 , polyhydramnios |
GENE, PHENOTYPE |
PGR_1, PGR_2 |
| Normalized Genes and Phenotypes | Find Normalized Genes and Phenotypes (the observable physical properties of an organism) related entities | med_ner.human_phenotype.go_biobert |
protein complex oligomerization , defective platelet aggregation |
GO, HP |
PGR_1, PGR_2 |
| Radiology Clinical JSL-V2 | Find radiology related entities in clinical setting | med_ner.jsl.wip.clinical.rd |
Kidney_Disease, HDL, Diet, Test, Imaging_Technique, Triglycerides, Obesity, Duration, Weight, Social_History_Header, ImagingTest, Labour_Delivery, Disease_Syndrome_Disorder, Communicable_Disease, Overweight, Units, Smoking, Score, Substance_Quantity, Form, Race_Ethnicity, Modifier, Hyperlipidemia, ImagingFindings, Psychological_Condition, OtherFindings, Cerebrovascular_Disease, Date, Test_Result, VS_Finding, Employment, Death_Entity, Gender, Oncological, Heart_Disease, Medical_Device, Total_Cholesterol, ManualFix, Time, Route, Pulse, Admission_Discharge, RelativeDate, O2_Saturation, Frequency, RelativeTime, Hypertension, Alcohol, Allergen, Fetus_NewBorn, Birth_Entity, Age, Respiration, Medical_History_Header, Oxygen_Therapy, Section_Header, LDL, Treatment, Vital_Signs_Header, Direction, BMI, Pregnancy, Sexually_Active_or_Sexual_Orientation, Symptom, Clinical_Dept, Measurements, Height, Family_History_Header, Substance, Strength, Injury_or_Poisoning, Relationship_Status, Blood_Pressure, Drug, Temperature, ,EKG_Findings, Diabetes, BodyPart, Vaccine, Procedure, Dosage |
Dataset by John Snow Labs, | |
| General Medical Terms | Find general medical terms and medical entities. | med_ner.medmentions |
Qualitative_Concept, Organization, Manufactured_Object, Amino_Acid, Peptide_or_Protein, Pharmacologic_Substance, Professional_or_Occupational_Group, Cell_Component, Neoplastic_Process, Substance, Laboratory_Procedure, Nucleic_Acid_Nucleoside_or_Nucleotide, Research_Activity, Gene_or_Genome, Indicator_Reagent_or_Diagnostic_Aid, Biologic_Function, Chemical, Mammal, Molecular_Function, Quantitative_Concept, Prokaryote, Mental_or_Behavioral_Dysfunction, Injury_or_Poisoning, Body_Location_or_Region, Spatial_Concept, Nucleotide_Sequence, Tissue, Pathologic_Function, Body_Substance, Fungus, Mental_Process, Medical_Device, Plant, Health_Care_Activity, Clinical_Attribute, Genetic_Function, Food, Therapeutic_or_Preventive_Procedure, Body_Part_Organ, Organ_Component, Geographic_Area, Virus, Biomedical_or_Dental_Material, Diagnostic_Procedure, Eukaryote, Anatomical_Structure, Organism_Attribute, Molecular_Biology_Research_Technique, Organic_Chemical, Cell, Daily_or_Recreational_Activity, Population_Group, Disease_or_Syndrome, Group, Sign_or_Symptom, Body_System |
MedMentions |
Assertion Domains and Models Overview¶
Named Entities extracted by an NER model can be further classified into sub-classes or statuses, depending on the context of the sentence. See the following two examples :
- Billy hates having a
headache - Billy has a
headache - Billy said his father has regular
headaches
All sentences have the entity headache which is of class disease.
But there is a semantic difference on what the actual status of the disease mentioned in text is. In the first and third sentence, Billy has no headache, but in the second sentence Billy actually has a sentence.
The Entity Assertion Algorithms provided by JSL solve this problem. The disease entity can be classified into ABSENT for the first case and into PRESENT for the second case. The third case can be classified into PRESENT IN FAMILY.
This has immense implications for various data analytical approaches in the helathcare domain.
I.e. imagine you want you want to make a study about hearth attacks and survival rate of potential procedures. You can process all your digital patient notes with an Medical NER model and filter for documents that have the Hearth Attack entity.
But your collected data will have wrong data entries because of the above mentioned Entity status problem. You cannot deduct that a document is talking about a patient having a hearth attack, unless you assert that the problem is actually there which is what the Resolutions algorithms do for you.
Keep in mind: This is a simplified example, entities should actually be mapped to their according Terminology (ICD-10-CM/ICD-10-PCS, etc..) to solve disambiguity problems and based on their codes all analysis should be performed
This algorithm is provided by Spark NLP for Healthcare's AssertionDLModel
| Domain | Description | Spell | Predicted Entities | Examples | Reference Dataset |
|---|---|---|---|---|---|
| Radiology | Predict status of Radiology related entities | assert.radiology |
Confirmed, Negative, Suspected |
- Confirmed: X-Ray scan shows cancer in lung. - Negative : X-Ray scan shows no sign of cancer in lung. - Suspected :X-Ray raises suspicion of cancer in lung but does not confirm it. |
Internal Dataset by Annotated by John Snow Labs |
| Healthcare/Clinical extended and Family JSL powerd | Predict status of, Healthcare/Clinical/Family related entities. Additional training with JSL Dataset | assert.jsl |
Present, Absent, Possible, Planned, Someoneelse, Past, Family, Hypotetical |
- Present: Patient diagnosed with cancer in 1999 - Absent: No sign of cancer was shown by the scans - Possible: Tests indicate patient might have cancer - Planned: CT-Scan is scheduled for 23.03.1999 - Someoneelse: The patient gave Aspirin to daugther. - Past: The patient has no more headaches since the operation - Family: The patients father has cancer. - Hypotetical:Death could be possible. |
2010 i2b2 + Data provided by JSL |
| Healthcare/Clinical JSL powerd | Predict status of Healthcare/Clinical related entities. Additional training with JSL Dataset | assert.jsl_large |
present, absent, possible, planned, someoneelse, past |
- present: Patient diagnosed with cancer in 1999 - absent: No sign of cancer was shown by the scans - possible: Tests indicate patient might have cancer - planned: CT-Scan is scheduled for 23.03.1999 - someoneelse: The patient gave Aspirin to daugther - past: The patient has no more headaches since the operation |
2010 i2b2 + Data provided by JSL |
| Healthcare/Clinical classic | Predict status of Healthcare/Clinical related entities | assert.biobert |
present , absent, possible, conditional, associated_with_someone_else ,hypothetical |
- present: Patient diagnosed with cancer in 1999 - absent: No sign of cancer was shown by the scans - possible: Tests indicate patient might have cancer - conditional If the test is positive, patient has AIDS- associated_with_someone_else: The patients father has cancer. - hypothetical :Death could be possible. |
2010 i2b2 |
Resolution Domains Models Overview¶
Named entities are sub-strings in a text that can be classified into catogires of a domain. For example, in the String
"Tesla is a great stock to invest in " , the sub-string "Tesla" is a named entity, it can be classified with the label company by an ML algorithm.
Named entities can easily be extracted by the various pre-trained Deep Learning based NER algorithms provided by NLU.
After extracting named entities an entity resolution algorithm can be applied to the extracted named entities. The resolution algorithm classifies each extracted entitiy into a class, which reduces dimensionality of the data and has many useful applications. For example :
- "Tesla is a great stock to invest in "
- "TSLA is a great stock to invest in "
- "Tesla, Inc is a great company to invest in"
The sub-strings Tesla , TSLA and Tesla, Inc are all named entities, that are classified with the labeld company by the NER algorithm. It tells us, all these 3 sub-strings are of type company, but we cannot yet infer that these 3 strings are actually referring to literally the same company.
This exact problem is solved by the resolver algorithms, it would resolve all these 3 entities to a common name, like a company ID. This maps every reference of Tesla, regardless of how the string is represented, to the same ID.
This example can analogusly be expanded to healthcare any any other text problems. In medical documents, the same disease can be referenced in many different ways.
With NLU Healthcare you can leverage state of the art pre-trained NER models to extract Medical Named Entities (Diseases, Treatments, Posology, etc..) and resolve these to common healthcare disease codes.
This algorithm is provided by Spark NLP for Healthcare's SentenceEntitiyResolver
| Domain/Terminology | Description | Sample NLU Spells | Sample Entities | Sample Predicted Codes | Reference Links |
|---|---|---|---|---|---|
| ICD-10 / ICD-10-CM (International Classification of Diseases - Clinical Modification) | Get ICD-10-CM codes of Medical and Clinical Entities. The ICD-10 Clinical Modification (ICD-10-CM) is a modification of the ICD-10, authorized by the World Health Organization, used as a source for diagnosis codes in the U.S. Be aware, ICD10-CM is often referred to as ICD10 |
resolve.icd10cm.augmented |
hypertension , gastritis |
I10, K2970 |
ICD-10-CM , WHO ICD-10-CM |
| ICD-10-PCS (International Classification of Diseases - Procedure Coding System) | Get ICD-10-PCS codes of Medical and Clinical Entities. The International Classification of Diseases, Procedure Coding System (ICD-10-PCS), is a U.S. cataloging system for procedural code It is maintaining by Centers for Medicare & Medicaid Services |
resolve.icd10pcs |
hypertension , gastritis |
DWY18ZZ, 04723Z6 |
ICD10-PCS, CMS ICD-10-PCS |
| ICD-O (International Classification of Diseases, Oncollogy) Topography & Morphology codes | Get ICD-0 codes of Medical and Clinical Entities. The International Classification of Diseases for Oncology (ICD-O), is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases. |
resolve.icdo.base |
metastatic lung cancer |
9050/3+C38.3, 8001/3+C39.8 |
ICD-O Histology Behaviour dataset |
| HCC (Hierachical Conditional Categories) | Get HCC codes of Medical and Clinical Entities. Hierarchical condition category (HCC) relies on ICD-10 coding to assign risk scores to patients. Along with demographic factors (such as age and gender), insurance companies use HCC coding to assign patients a risk adjustment factor (RAF) score. |
resolve.hcc |
hypertension , gastritis |
139, 188 |
HCC |
| ICD-10-CM + HCC Billable | Get ICD-10-CM and HCC codes of Medical and Clinical Entities. |
resolve.icd10cm.augmented_billable |
metastatic lung cancer |
C7800 + ['1', '1', '8'] |
ICD10-CM HCC |
| CPT (Current Procedural Terminology) | Get CPT codes of Medical and Clinical Entities. The Current Procedural Terminology(CPT) is developed by the American Medical Association (AMA) and used to assign codes to medical procedures/services/diagonstics. The codes are used to derive the amount of payment a healthcare provider may receives from insurance companies for the provided service.receives |
resolve.cpt.procedures_measurements |
calcium score, heart surgery |
82310, 33257 |
CPT |
| LOINC (Logical Observation Identifiers Names and Codes) | Get LOINC codes of Medical and Clinical Entities. Logical Observation Identifiers Names and Codes (LOINC) developed by theU.S. organization Regenstrief Institute |
resolve.loinc |
acute hepatitis ,obesity |
28083-4,50227-8 |
LOINC |
| HPO (Human Phenotype Ontology) | Get HPO codes of Medical and Clinical Entities. |
resolve.HPO |
cancer, bipolar disorder |
0002664, 0007302, 0100753 |
HPO |
| UMLS (Unified Medical Language System) CUI | Get UMLS codes of Medical and Clinical Entities. |
resolve.umls.findings |
vomiting, polydipsia, hepatitis |
C1963281, C3278316, C1963279 |
UMLS |
| SNOMED International (Systematized Nomenclature of Medicine) | Get SNOMED (INT) codes of Medical and Clinical Entities. |
resolve.snomed.findings_int |
hypertension |
148439002 |
SNOMED |
| SNOMED CT (Clinical Terms) | Get SNOMED (CT) codes of Medical and Clinical Entities. |
resolve.snomed.findings |
hypertension |
73578008 |
SNOMED |
| SNOMED Conditions | Get SNOMED Conditions codes of Medical and Clinical Entities. |
resolve.snomed_conditions |
schizophrenia |
58214004 |
SNOMED |
| RxNorm and RxCUI (Concept Uinque Indentifier) | Get Normalized RxNorm and RxCUI codes of Medical, Clinical and Drug Entities. |
resolve.rxnorm |
50 mg of eltrombopag oral |
825427 |
[RxNorm Overview] [November 2020 RxNorm Clinical Drugs ontology graph] |
Relation Extraction Domains and Models Overview¶
Most sentences and documents have a lof of entities which can be extracted with NER. These entities alone already provide a lot of insight and information about your data, but there is even more information extractable...
Each entity in a sentence always has some kind of relationship to every other entity in the sentence. In other words, each entity pair has a relationship ! If a sentence has N entities, there are NxN potential binary relationships and NxNxK for k-ary relationships.
The RelationExtraction Algortihms provided by JSL classify for each pair of entities what the type of relationship between is, based on some domain.
A concrete use-case example:
Lets say you want to analyze the survival rate of amputation procedures peformed on the left hand.
Using just NER, we could find all documents that mention the entity amputation , left and hand.
The collected data will have wrong entries, imagine the following clinical note :
- The patients
leftfootand hisrighthandwere amputated`
This record would be part of our analysis, if we just use NER with the above mentioned filtering.
The RelationExtraction Algorithms provided by JSL solves this problem. The relation.bodypart.directions model can classify for each entity pair, wether they are related or not.
In our example, it can classify that left and foot are related and that right and hand are related. Based on these classified relationships, we can easily enhance our filters and make sure no wrong records are used for our surival rate analysis.
But what about the following sentence?
- The patients
lefthandwas saved but hisfootwasamputated
This would pass all the NER and Relationship filters defined sofar. But we can easily cover this case by using the relation.bodypart.procedures model, which can predict wether a procedure entity was peformed on some bodypart or not. In the last example, it can predict foot and amputated are related, buthand and amputated are not in relationship, aswell as left and amputated (since every entity pair gets a prediction).
In conclusion, we can adjust our filters to additionaly verify that the amputation procedure is peformed on a hand and that this hand is in relationship with a direction entity with the value left.
Keep in mind: This is a simplified example, entities should actually be mapped to their according Terminology (ICD-10-CM/ICD-10-PCS, etc..) to solve disambiguity problems and based on their codes all analysis should be performed
These algorithm are provided by Spark NLP for Healthcare's RelationExtraction and RelationExtractionDL
Relation Extraction Domains and Models examples¶
| Domain | Description | Sample NLU Spells | Predictable Relationships and Explanation |
|---|---|---|---|
| Dates and Clinical Entities | Predict binary temporal relationship between Date Entities and Clinical Entities |
relation.date |
- 1 for Date Entity and Clinical Entity are related. - 0 for Date Entity and Clinical Entity are not related |
| Body Parts and Directions | Predict binary direction relationship between Bodypart Entities and Direction Entities |
relation.bodypart.direction |
- 1 for Body Part and Direction are related - 0 for Body Part and Direction are not related |
| Body Parts and Problems | Predict binary location relationship between Bodypart Entities and Problem Entities |
relation.bodypart.problem |
- 1 for Body Part and Problem are related - 0 for Body Part and Problem are not related |
| Body Parts and Procedures | Predict binary application relationship between Bodypart Entities and Procedure Entities |
relation.bodypart.procedure |
- 1 for Body Part and Test/Procedure are related - 0 for Body Part and Test/Procedure are not related |
| Adverse Effects between drugs (ADE) | Predict binary effect relationship between Drugs Entities and Adverse Effects/Problem Entities |
relation.ade |
- 1 for Adverse Event Entity and Drug are related - 0 for Adverse Event Entity and Drug are not related |
| Phenotype abnormalities,Genes and Diseases | Predict binary caused by relationship between Phenotype Abnormality Entities, Gene Entities and Disease Entities |
relation.humen_phenotype_gene |
- 1 for Gene Entity and Phenotype Entity are related - 0 for Gene Entity and Phenotype Entity are not related |
| Temporal events | Predict multi-class temporal relationship between Time Entities and Event Entities |
relation.temporal_events |
- AFTER if Any Entity occured after Another Entity - BEFORE if Any Entity occured before Another Entity - OVERLAP if Any Entity during Another Entity |
| Dates and Tests/Results | Predict multi-class temporal cause,reasoning and conclusion relationship between Date Entities, Test Entities and Result Entities |
relation.test_result_date |
- relation.test_result_date - is_finding_of for Medical Entity is found because of Test Entity - is_result_of for Medical Entity reason for doing Test Entity - is_date_of for Date Entity relates to time of Test/Result - 0 : No relationship |
| Clinical Problem, Treatment and Tests | Predict multi-class cause,reasoning and effect relationship between Treatment Entities, Problem Entities and Test Entities |
relation.clinical |
- TrIP: A certain treatment has improved/cured a medical problem - TrWP: A patient's medical problem has deteriorated or worsened because of treatment - TrCP: A treatment caused a medical problem - TrAP: A treatment administered for a medical problem - TrNAP: The administration of a treatment was avoided because of a medical problem - TeRP: A test has revealed some medical problem - TeCP: A test was performed to investigate a medical problem - PIP: Two problems are related to each other |
| DDI Effects of using Multiple Drugs (Drug Drug Interaction) | Predict multi-class effects, mechanisms and reasoning for DDI effects(Drug Drug Interaction) relationships between Drug Entities |
relation.drug_drug_interaction |
- DDI-advise when an advice/recommendation regarding aDrug Entity and Drug Entity is given - DDI-effect when Drug Entity and Drug Entity have an effect on the human body (pharmacodynamic mechanism). Including a clinical finding, signs or symptoms, an increased toxicity or therapeutic failure. - DDI-int when effect between Drug Entity and Drug Entity is already known and thus provides no additional information. - DDI-mechanism when Drug Entity and Drug Entity are affected by an organism (pharmacokinetic). Such as the changes in levels or concentration in a drug. Used for DDIs that are described by their PK mechanism - DDI-false when a Drug Entity and Drug Entity have no interaction mentioned in the text. |
| Posology (Drugs, Dosage, Duration, Frequency,Strength) | Predict multi-class posology relationships between Drug Entities,Dosage Entities,Strength Entities,Route Entities, Form Entities, Duration Entities and Frequency Entities |
relation.posology |
- DRUG-ADE if Problem Entity Adverse effect of Drug Entity - DRUG-DOSAGE if Dosage Entity refers to a Drug Entity - DRUG-DURATION if Duration Entity refers to a Drug Entity - DRUG-FORM if Mode/Form Entity refers to intake form of Drug Entity - DRUG-FREQUENCY if Frequency Entity refers to usage of Drug Entity - DRUG-REASON if Problem Entity is reason for taking Drug Entity - DRUG-ROUTE if Route Entity refer to administration method of Drug Entity - DRUG-STRENGTH if Strength Entity refers to Drug Entity |
| Chemicals and Proteins | Predict Regulator, Upregulator, Downregulator, Agonist, Antagonist, Modulator, Cofactor, Substrate relationships between Chemical Entities and Protein Entities |
relation.chemprot |
- CPR:1 if One ChemProt Entity is Part of of Another ChemProt Entity - CPR:2 if One ChemProt Entity is Regulator (Direct or Indirect) of Another ChemProt Entity - CPR:3 if One ChemProt Entity is Upregulator/Activator/Indirect Upregulator of Another ChemProt Entity - CPR:4 if One ChemProt Entity is Downregulator/Inhibitor/Indirect Downregulator of Another ChemProt Entity - CPR:5 if One ChemProt Entity is Agonist of Another ChemProt Entity - CPR:6 if One ChemProt Entity is Antagonist of Another ChemProt Entity - CPR:7 if One ChemProt Entity is Modulator (Activator/Inhibitor) of Another ChemProt Entity - CPR:8 if One ChemProt Entity is Cofactor of Another ChemProt Entity - CPR:9 if One ChemProt Entity is Substrate and product of of Another ChemProt Entity - CPR:10 if One ChemProt Entity is Not Related to Another ChemProt Entity |
Relation Domain Examples¶
| Domain | Sentence With Relationships | Predicted Relationships for Sample Sentence | Reference Links |
|---|---|---|---|
| Dates and Clinical Entities | This 73 y/o patient had CT on 1/12/95, with cognitive decline since 8/11/94. |
- 1 for CT and1/12/95 - 0 for cognitive decline and 1/12/95 - 1 for cognitive decline and 8/11/94 |
Internal Dataset by Annotated by John Snow Labs |
| Body Parts and Directions | MRI demonstrated infarction in the upper - brain stem , left cerebellum and right basil ganglia |
- 1 for uppper and brain stem - 0 for upper and cerebellum - 1 for left and cerebellum |
Internal Dataset by Annotated by John Snow Labs |
| Body Parts and Problems | Patient reported numbness in his left hand and bleeding from ear. |
- 1 for numbness and hand - 0 for numbness and ear - 1 for bleeding and ear |
Internal Dataset by Annotated by John Snow Labs |
| Body Parts and Procedures | The chest was scanned with portable ultrasound and amputation was performed on foot |
- 1 for chest and portable ultrasound - 0 for chest and amputation - 1 for foot and amputation |
Internal Dataset by Annotated by John Snow Labs |
| Adverse Effects between drugs (ADE) | Taking Lipitor for 15 years, experienced much sever fatigue! Doctor moved me to voltaren 2 months ago , so far only experienced cramps |
- 1 for sever fatigue and Liptor- 0 for sever fatigue and voltaren- 0 for cramps and Liptor- 1 for cramps and voltaren |
Internal Dataset by Annotated by John Snow Labs |
| Phenotype abnormalities,Genes and Diseases | She has a retinal degeneration, hearing loss and renal failure, short stature, Mutations in the SH3PXD2B gene coding for the Tks4 protein are responsible for the autosomal recessive. |
- 1 for hearing loss and SH3PXD2B- 0 for retinal degeneration and hearing loss- 1 for retinal degeneration and autosomal recessive |
PGR aclAntology |
| Temporal events | She is diagnosed with cancer in 1991. Then she was admitted to Mayo Clinic in May 2000 and discharged in October 2001 |
- OVERLAP for cancer and 1991 - AFTER for additted and Mayo Clinic - BEFORE for admitted and discharged |
Temporal JSL Dataset and n2c2 |
| Dates and Tests/Results | On 23 March 1995 a X-Ray applied to patient because of headache, found tumor in brain |
- is_finding_of for tumor and X-Ray - is_result_of for headache and X-Ray - is_date_of for 23 March 1995 and X-Ray |
Internal Dataset by Annotated by John Snow Labs |
| Clinical Problem, Treatment and Tests | - TrIP : infection resolved with antibiotic course - TrWP : the tumor was growing despite the drain - TrCP: penicillin causes a rash - TrAP:Dexamphetamine for narcolepsy - TrNAP: Ralafen was not given because of ulcers - TeRP: an echocardiogram revealed a pericardial effusion - TeCP: chest x-ray for pneumonia - PIP: Azotemia presumed secondary to sepsis |
- TrIP for infection and antibiotic course - TrWP for tumor and drain - TrCP for penicillin andrash - TrAP for Dexamphetamine and narcolepsy - TrNAP for Ralafen and ulcers - TeRP for echocardiogram and pericardial effusion - TeCP for chest x-ray and pneumonia - PIP for Azotemia and sepsis |
2010 i2b2 relation challenge |
| DDI Effects of using Multiple Drugs (Drug Drug Interaction) | - DDI-advise: UROXATRALshould not be used in combination with other alpha-blockers - DDI-effect: Chlorthalidone may potentiate the action of other antihypertensive drugs - DDI-int : The interaction of omeprazole and ketoconazole has been established - DDI-mechanism : Grepafloxacin may inhibit the metabolism of theobromine - DDI-false : Aspirin does not interact with Chlorthalidone |
- DDI-advise for UROXATRAL and alpha-blockers - DDI-effect for Chlorthalidone and antihypertensive drugs - DDI-int for omeprazole and ketoconazole - DDI-mechanism for Grepafloxacin and theobromine - DDI-false for Aspirin and Chlorthalidone |
DDI Extraction corpus |
| Posology (Drugs, Dosage, Duration, Frequency,Strength) | - DRUG-ADE: had a headache after taking Paracetamol - DRUG-DOSAGE: took 0.5ML ofCelstone - DRUG-DURATION: took Aspirin daily for two weeks - DRUG-FORM: took Aspirin as tablets - DRUG-FREQUENCY : Aspirin usage is weekly - DRUG-REASON : Took Aspirin because of headache - DRUG-ROUTE: Aspirin taken orally - DRUG-STRENGTH: 2mg of Aspirin |
- DRUG-ADE for headache and Paracetamol - DRUG-DOSAGE for 0.5ML and Celstone - DRUG-DURATION for Aspirin and for two weeks - DRUG-FORM for Aspirin and tablets - DRUG-FREQUENCY for Aspirin and weekly - DRUG-REASON for Aspirin and headache - DRUG-ROUTE for Aspirin and orally - DRUG-STRENGTH for 2mg and Aspirin |
Magge, Scotch, Gonzalez-Hernandez (2018) |
| Chemicals and Proteins | - CPR:1 (Part of) : The amino acid sequence of the rabbit alpha(2A)-adrenoceptor has many interesting properties. - CPR:2 (Regulator) : Triacsin inhibited ACS activity - CPR:3 (Upregulator) : Ibandronate increases the expression of the FAS gene - CPR:4 (Downregulator) : Vitamin C treatment resulted in reduced C-Rel nuclear translocation - CPR:5 (Agonist) : Reports show tricyclic antidepressants act as agnonists at distinct opioid receptors - CPR:6 (Antagonist) : GDC-0152 is a drug triggers tumor cell apoptosis by selectively antagonizing LAPs - CPR:7 (Modulator) : Hydrogen sulfide is a allosteric modulator of ATP-sensitive potassium channels - CPR:8 (Cofactor) : polyinosinic:polycytidylic acid and the IFNα/β demonstrate capability of endogenous IFN. - CPR:9 (Substrate) : ZIP9 plays an important role in the transport and toxicity of Cd(2+) cells - CPR:10 (Not Related): Studies indicate that GSK-3β inhibition by palinurin cannot be competed out by ATP |
- CPR:1 (Part of) for amino acid and rabbit alpha(2A)-adrenoceptor - CPR:2 (Regulator) for Triacsin and ACS - CPR:3 (Upregulator) for Ibandronate and FAS gene - CPR:4 (Downregulator) for Vitamin C and C-Rel - CPR:5 (Agonist) for tricyclic antidepressants and opioid receptors - CPR:6 (Antagonist) (Antagonist) for GDC-0152 and LAPs - CPR:7 (Modulator) for Hydrogen sulfide and ATP-sensitive potassium channels - CPR:8 (Cofactor) for polyinosinic:polycytidylic acid and IFNα/β - CPR:9 (Substrate) for ZIP9 and Cd(2+) cells - CPR:10 (Not Related) for GSK-3β and ATP |
ChemProt Paper |
Install NLU¶
In [ ]:
!wget https://setup.johnsnowlabs.com/nlu/colab.sh -O - | bash
import nlu
--2022-04-15 12:38:41-- https://setup.johnsnowlabs.com/nlu/colab.sh
Resolving setup.johnsnowlabs.com (setup.johnsnowlabs.com)... 51.158.130.125
Connecting to setup.johnsnowlabs.com (setup.johnsnowlabs.com)|51.158.130.125|:443... connected.
HTTP request sent, awaiting response... 302 Moved Temporarily
Location: https://raw.githubusercontent.com/JohnSnowLabs/nlu/master/scripts/colab_setup.sh [following]
--2022-04-15 12:38:42-- https://raw.githubusercontent.com/JohnSnowLabs/nlu/master/scripts/colab_setup.sh
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
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Saving to: ‘STDOUT’
- 0%[ ] 0 --.-KB/s Installing NLU 3.4.3rc2 with PySpark 3.0.3 and Spark NLP 3.4.2 for Google Colab ...
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Fetched 13.8 MB in 4s (3,670 kB/s)
Reading package lists... Done
tar: spark-3.0.2-bin-hadoop2.7.tgz: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
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Building wheel for pyspark (setup.py) ... done
Collecting nlu_tmp==3.4.3rc10
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Installing collected packages: nlu-tmp
Successfully installed nlu-tmp-3.4.3rc10
Setup Healthcare License for NLU¶
See authorization docs for more info. Make sure to restart your Python Kernel session if you run into issues.
Authorize via spark_nlp_for_healthcare.json¶
Either upload spark_nlp_for_healthcare.json to the default directory and NLU will automatically authorize
In [ ]:
%%capture
# Get Licensed via file upload, you need to upload spark_nlp_for_healthcare.json
import nlu
import json
from google.colab import files
license_keys = files.upload()
with open(list(license_keys.keys())[0]) as f:
license_keys = json.load(f)
Saving spark_nlp_for_healthcare.json to spark_nlp_for_healthcare.json
Authorize manually (ALTERNATIVE)¶
You can also read out all the secrets from spark_nlp_for_healthcare.json or from the E-Mail originally sent to you and enter them into the variables below
In [ ]:
%%capture
# Or manually enter secrets
# import nlu
# SPARK_NLP_LICENSE = '?????'
# AWS_ACCESS_KEY_ID = '?????'
# AWS_SECRET_ACCESS_KEY = '?????'
# JSL_SECRET = '?????'
# nlu.auth(SPARK_NLP_LICENSE,AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY,JSL_SECRET)
Medical Named Entity Recognizers¶
NER Domains and Models Overview¶
Named entities are sub-strings in a text that can be classified into catogires of a domain. For example, in the String
"Tesla is a great stock to invest in " , the sub-string "Tesla" is a named entity, it can be classified with the label company by an ML algorithm.
Named entities can easily be extracted by the various pre-trained Deep Learning based NER algorithms provided by NLU.
NER models can be trained for many different domains and aquire expert domain knowledge in each of them. JSL provides a wide array of experts for various Medical, Helathcare and Clinical domains
This algorithm is provided by Spark NLP for Healthcare's MedicalNerModel
| Domain | Description | Sample NLU Spells | Sample Entities | Sample Predicted Labels | Reference Links |
|---|---|---|---|---|---|
| ADE (Adverse Drug Events) | Find adverse drug event (ADE) related entities | med_ner.ade_biobert |
Aspirin , vomiting |
DRUG, ADE |
CADEC, Twimed |
| Anatomy | Find body parts, anatomical sites a nd reference related entities | med_ner.anatomy |
tubules, nasopharyngeal aspirates, embryoid bodies, NK cells, Mitochondrial, tracheoesophageal fistulas, heart, colon cancer, cervical, central nervous system |
Tissue_structure, Organism_substance, Developing_anatomical_structure, Cell, Cellular_component, Immaterial_anatomical_entity, organ, Pathological_formation, Organism_subdivision, Anatomical_system |
AnEM |
| Cellular/Molecular Biology | Find Genes, Molecules, Cell or general Biology related entities | med_ner.cellular.biobert |
human T-cell leukemia virus type 1 Tax-responsive , primary T lymphocytes, E1A-immortalized, Spi-B mRNA, zeta-globin |
DNA, Cell_type, Cell_line, RNA, Protein |
JNLPBA |
| Chemical/Genes/Proteins | Find Chemical, Gene and Protein related entities | med_ner.chemprot.clinical |
nitrogen , β-amyloid , NF-kappaB |
CHEMICAL, GENE-Y, GENE-N |
ChemProt |
| Chemical Compounds | Find general chemical compound related entities | med_ner.chemicals |
resveratrol , β-polyphenol |
CHEM |
Dataset by John Snow Labs |
| Drug Chemicals | Find chemical and drug related entities | med_ner.drugs |
potassium , anthracyclines, taxanes |
DrugChem.DrugChem.DrugChem |
i2b2 + FDA |
| Posology/Drugs | Find posology and drug related entities | med_ner.posology.biobert |
5000 units, Aspirin, 14 days, tablets, daily, topically, 30 mg |
DOSAGE, DRUG, DURATION, FORM, FREQUENCY, ROUTE, STRENGTH. |
i2b2 + FDA |
| Risk Factors | Find risk factor of patient related entities | med_ner.risk_factors.biobert |
coronary artery disease, hypertension, Smokes 2 packs of cigarettes per day, morbid obesity, Actos, Works in School, diabetic, diabetic |
CAD, HYPERTENSION, SMOKER, OBESE, FAMILY_HIST, MEDICATION, PHI, HYPERLIPIDEMIA, DIABETES |
De-identification and Heart Disease Risk Factors Challenge datasets |
| cancer Genetics | Find cancer and genetics related entities | med_ner.cancer |
human, Kir 3.3, GIRK3, potassium, GIRK, chromosome 1q21-23, pancreas, tissues, fat andskeletal muscle, KCNJ9, Type II, breast cancer, patients, anthracyclines, taxanes, vinorelbine, patients, breast, vinorelbine inpatients, anthracyclines |
Amino_acid, Anatomical_system, cancer, Cell, Cellular_component, Developing_anatomical_Structure , Gene_or_gene_product, Immaterial_anatomical_entity, Multi-tissue_structure, Organ, Organism , Organism_subdivision, Simple_chemical, Tissue |
CG TASK of BioNLP 2013 |
| Diseases | Find disease related entities | med_ner.diseases.biobert |
the cyst, a large Prolene suture, a very small incisional hernia, the hernia cavity, omentum, the hernia, the wound lesion, The lesion, the existing scar, the cyst, the wound, this cyst down to its base, a small incisional hernia, The cyst |
Disease |
CG TASK of BioNLP 2013 |
| Bacterial Species | Find bacterial species related entities | med_ner.bacterial_species |
Neisseria wadsworthii, N. bacilliformis, Spirochaeta litoralis |
SPECIES |
Dataset by John Snow Labs |
| Medical Problem/Test/Treatment | Find medical problem,test and treatment related entities | med_ner.healthcare |
respiratory tract infection , Ourexpression studies, atorvastatin |
PROBLEM, TEST, TREATMENT |
i2b2 |
| Clinical Admission Events | Find clinical admission event related entities | med_ner.admission_events |
2007, 12 AM, Headache, blood sample, presented, emergency room, daily |
DATE, TIME, PROBLEM, TEST, TREATMENT, OCCURENCE, CLINICAL_DEPT, EVIDENTIAL, DURATION, FREQUENCY, ADMISSION, DISCHARGE |
Custom i2b2, enriched with Events |
| Genetic Variants | Find genetic variant related entities | en.med_ner.genetic_variants |
rs1061170, p.S45P, T13046C |
DNAMutation, ProteinMutation, SNP |
TMVAR |
| PHI (Protected Healthcare Information) | Find PHI(Protected Healthcare) related entities | en.med_ner.deid |
2093-01-13, David Hale, Hendrickson,</br> Ora, 7194334, 01/13/93, Oliveira, 25-year-old, 1-11-2000, Cocke County Baptist Hospital, 0295 Keats Street., (302) 786-5227, Brothers Coal-Mine |
MEDICALRECORD, ORGANIZATION, DOCTOR, USERNAME, PROFESSION, HEALTHPLAN, URL, CITY, DATE, LOCATION-OTHER, STATE, PATIENT, DEVICE, COUNTRY, ZIP, PHONE, HOSPITAL, EMAIL, IDNUM, SREET, BIOID, FAX, AGE |
n2c2 i2b2-PHI |
| Social Determinants / Demographic Data | Find Social Determinants and Demographic Data Related Entities | med_ner.jsl.enriched |
21-day-old, male, congestion, mom, suctioning yellow discharge, she, problems with his breathing, perioral cyanosis, retractions, mom, Tylenol, His, his, respiratory congestion, He, tired, fussy, albuterol |
Age, Diagnosis, Dosage, Drug_Name, Frequency, Gender, Lab_Name, Lab_Result, Symptom_Name |
Dataset by John Snow Labs |
| General Clinical | Find General Clinical Entities | med_ner.jsl.wip.clinical.modifier |
28-year-old, female, gestational, diabetes, mellitus, eight, years, prior, type, two, diabetes, mellitus, T2DM, HTG-induced, pancreatitis, three, years, prior, acute, hepatitis, obesity, body, mass, index, BMI, kg/m2, polyuria, polydipsia, poor, appetite, vomiting, Two, weeks, prior, she, five-day, course |
Injury_or_Poisoning, Direction, Test, Admission_Discharge, Death_Entity, Relationship_Status, Duration, Respiration, Hyperlipidemia, Birth_Entity, Age, Labour_Delivery, Family_History_Header, BMI, Temperature, Alcohol, Kidney_Disease, Oncological, Medical_History_Header, Cerebrovascular_Disease, Oxygen_Therapy, O2_Saturation, Psychological_Condition, Heart_Disease, Employment, Obesity, Disease_Syndrome_Disorder, Pregnancy, ImagingFindings, Procedure, Medical_Device, Race_Ethnicity, Section_Header, Symptom, Treatment, Substance, Route, Drug_Ingredient, Blood_Pressure, Diet, External_body_part_or_region, LDL, VS_Finding, Allergen, EKG_Findings, Imaging_Technique, Triglycerides, RelativeTime, Gender, Pulse, Social_History_Header, Substance_Quantity, Diabetes, Modifier, Internal_organ_or_component, Clinical_Dept, Form, Drug_BrandName, Strength, Fetus_NewBorn, RelativeDate, Height, Test_Result, Sexually_Active_or_Sexual_Orientation, Frequency, Time, Weight, Vaccine, Vital_Signs_Header, Communicable_Disease, Dosage, Overweight, Hypertension, HDL, Total_Cholesterol, Smoking, ` |
Dataset by John Snow Labs |
| Radiology | Find Radiology related entities | med_ner.radiology.wip_clinical |
Bilateral, breast, ultrasound, ovoid mass, 0.5 x 0.5 x 0.4, cm, anteromedial aspect, left, shoulder, mass, isoechoic echotexture, muscle, internal color flow, benign fibrous tissue, lipoma |
ImagingTest, Imaging_Technique, ImagingFindings, OtherFindings, BodyPart, Direction, Test, Symptom, Disease_Syndrome_Disorder, Medical_Device, Procedure, Measurements, Units |
Dataset by John Snow Labs, MIMIC-CXR and MT Radiology texts |
| Radiology Clinical JSL-V1 | Find radiology related entities in clinical setting | med_ner.radiology.wip_greedy_biobert |
Bilateral, breast, ultrasound, ovoid mass, 0.5 x 0.5 x 0.4, cm, anteromedial aspect, left, shoulder, mass, isoechoic echotexture, muscle, internal color flow, benign fibrous tissue, lipoma |
Test_Result, OtherFindings, BodyPart, ImagingFindings, Disease_Syndrome_Disorder, ImagingTest, Measurements, Procedure, Score, Test, Medical_Device, Direction, Symptom, Imaging_Technique, ManualFix, Units |
Dataset by John Snow Labs, |
| Genes and Phenotypes | Find Genes and Phenotypes (the observable physical properties of an organism) related entities | med_ner.human_phenotype.gene_biobert |
APOC4 , polyhydramnios |
GENE, PHENOTYPE |
PGR_1, PGR_2 |
| Normalized Genes and Phenotypes | Find Normalized Genes and Phenotypes (the observable physical properties of an organism) related entities | med_ner.human_phenotype.go_biobert |
protein complex oligomerization , defective platelet aggregation |
GO, HP |
PGR_1, PGR_2 |
| Radiology Clinical JSL-V2 | Find radiology related entities in clinical setting | med_ner.jsl.wip.clinical.rd |
Kidney_Disease, HDL, Diet, Test, Imaging_Technique, Triglycerides, Obesity, Duration, Weight, Social_History_Header, ImagingTest, Labour_Delivery, Disease_Syndrome_Disorder, Communicable_Disease, Overweight, Units, Smoking, Score, Substance_Quantity, Form, Race_Ethnicity, Modifier, Hyperlipidemia, ImagingFindings, Psychological_Condition, OtherFindings, Cerebrovascular_Disease, Date, Test_Result, VS_Finding, Employment, Death_Entity, Gender, Oncological, Heart_Disease, Medical_Device, Total_Cholesterol, ManualFix, Time, Route, Pulse, Admission_Discharge, RelativeDate, O2_Saturation, Frequency, RelativeTime, Hypertension, Alcohol, Allergen, Fetus_NewBorn, Birth_Entity, Age, Respiration, Medical_History_Header, Oxygen_Therapy, Section_Header, LDL, Treatment, Vital_Signs_Header, Direction, BMI, Pregnancy, Sexually_Active_or_Sexual_Orientation, Symptom, Clinical_Dept, Measurements, Height, Family_History_Header, Substance, Strength, Injury_or_Poisoning, Relationship_Status, Blood_Pressure, Drug, Temperature, ,EKG_Findings, Diabetes, BodyPart, Vaccine, Procedure, Dosage |
Dataset by John Snow Labs, | |
| General Medical Terms | Find general medical terms and medical entities. | med_ner.medmentions |
Qualitative_Concept, Organization, Manufactured_Object, Amino_Acid, Peptide_or_Protein, Pharmacologic_Substance, Professional_or_Occupational_Group, Cell_Component, Neoplastic_Process, Substance, Laboratory_Procedure, Nucleic_Acid_Nucleoside_or_Nucleotide, Research_Activity, Gene_or_Genome, Indicator_Reagent_or_Diagnostic_Aid, Biologic_Function, Chemical, Mammal, Molecular_Function, Quantitative_Concept, Prokaryote, Mental_or_Behavioral_Dysfunction, Injury_or_Poisoning, Body_Location_or_Region, Spatial_Concept, Nucleotide_Sequence, Tissue, Pathologic_Function, Body_Substance, Fungus, Mental_Process, Medical_Device, Plant, Health_Care_Activity, Clinical_Attribute, Genetic_Function, Food, Therapeutic_or_Preventive_Procedure, Body_Part_Organ, Organ_Component, Geographic_Area, Virus, Biomedical_or_Dental_Material, Diagnostic_Procedure, Eukaryote, Anatomical_Structure, Organism_Attribute, Molecular_Biology_Research_Technique, Organic_Chemical, Cell, Daily_or_Recreational_Activity, Population_Group, Disease_or_Syndrome, Group, Sign_or_Symptom, Body_System |
MedMentions |
In [ ]:
pheno_pipe = nlu.load('med_ner.human_phenotype.gene_biobert')
pheno_pipe.predict("The APOC4 expression in this patient shows polyhydramnios, polyuria, nephrocalcinosis and hypokalemia")
ner_wikiner_glove_840B_300 download started this may take some time. Approximate size to download 14.8 MB [OK!] glove_840B_300 download started this may take some time. Approximate size to download 2.3 GB [OK!] sentence_detector_dl download started this may take some time. Approximate size to download 354.6 KB [OK!]
Out[ ]:
| document | entities_wikiner_glove_840B_300 | entities_wikiner_glove_840B_300_class | entities_wikiner_glove_840B_300_confidence | word_embedding_glove | |
|---|---|---|---|---|---|
| 0 | The APOC4 expression in this patient shows pol... | APOC4 | MISC | 0.8803 | [[-0.06767900288105011, 0.09451500326395035, -... |
In [ ]:
pheno_pipe.viz("The APOC4 expression in this patient shows polyhydramnios, polyuria, nephrocalcinosis and hypokalemia")
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip. Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue. To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
Collecting spark-nlp-display Downloading spark_nlp_display-1.9.1-py3-none-any.whl (95 kB) Requirement already satisfied: numpy in /usr/local/lib/python3.7/dist-packages (from spark-nlp-display) (1.21.5) Collecting svgwrite==1.4 Downloading svgwrite-1.4-py3-none-any.whl (66 kB) Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from spark-nlp-display) (1.3.5) Requirement already satisfied: ipython in /usr/local/lib/python3.7/dist-packages (from spark-nlp-display) (5.5.0) Requirement already satisfied: spark-nlp in /usr/local/lib/python3.7/dist-packages (from spark-nlp-display) (3.4.2) Requirement already satisfied: pygments in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (2.6.1) Requirement already satisfied: simplegeneric>0.8 in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (0.8.1) Requirement already satisfied: pickleshare in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (0.7.5) Requirement already satisfied: decorator in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (4.4.2) Requirement already satisfied: pexpect in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (4.8.0) Requirement already satisfied: traitlets>=4.2 in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (5.1.1) Requirement already satisfied: setuptools>=18.5 in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (57.4.0) Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /usr/local/lib/python3.7/dist-packages (from ipython->spark-nlp-display) (1.0.18) Requirement already satisfied: six>=1.9.0 in /usr/local/lib/python3.7/dist-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython->spark-nlp-display) (1.15.0) Requirement already satisfied: wcwidth in /usr/local/lib/python3.7/dist-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython->spark-nlp-display) (0.2.5) Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas->spark-nlp-display) (2018.9) Requirement already satisfied: python-dateutil>=2.7.3 in /usr/local/lib/python3.7/dist-packages (from pandas->spark-nlp-display) (2.8.2) Requirement already satisfied: ptyprocess>=0.5 in /usr/local/lib/python3.7/dist-packages (from pexpect->ipython->spark-nlp-display) (0.7.0) Installing collected packages: svgwrite, spark-nlp-display Successfully installed spark-nlp-display-1.9.1 svgwrite-1.4
The APOC4 MISC expression in this patient shows polyhydramnios, polyuria, nephrocalcinosis and hypokalemia