Understanding DeepPhe Output - DeepPhe/DeepPhe-Release GitHub Wiki
Using the .piper configuration file, various output writers can be added to the DeepPhe pipeline. These various writers can be used to answer questions such as:
-
What are the relevant biomarkers and mutations identified in ONE pathology report for a specific patient?
-
What are the relevant biomarkers and mutations identified in ALL pathology reports for a specific patient?
-
What treatments were identified in the reports?
etc...(more later)
Writers
PatientSummaryXnJsonFileWriter
DpheRelTableWriter
Configuration Options
SubDirectory=REL TableType=HTML
The files contain human readable information that list relations between two concepts for each patiennt.
| filename | section | description |
|---|---|---|
| reportName_rel_table.html | source | The source concept. |
| relation | The relation between the source and the target concept. | |
| target | The target concept. | |
| confidence | The confidence the system has in the relation. |
DpheTableWriter
Configuration Options
SubDirectory=TABLE TableType=HTML
The table output file format contains a human readable list of concepts for each report.
| filename | column | description |
|---|---|---|
| reportName_.table.html | DpheGroup | The group of the mention (e.g., Gene, Neoplasm,Tissue, Body Part) |
| Section | The section in which the concept was found. | |
| Span | The start and ending location of the characters in the report used to identify the concept. (e.g. 40,48). | |
| Negated | Whether the term is negated or not. | |
| Uncertain | Whether the term has modifiers that express uncertainty in the concept. | |
| Generic | ? | |
| URI | The ClassURI of the concept (e.g. VIMGene) | |
| Confidence | The confidence that the system has in correctly identifying the concept. | |
| Document Text | The document text used to identify the concept (e.g. VIMENTIN). |
EvalWriter
The eval writer writes single values for attributes that are use for evaluation of the pipeline.
| filename | section | description |
|---|---|---|
| patientId_cancer.csv | Patient_ID | |
| -record_id | ||
| -topography_major | ||
| laterality | ||
| grade | ||
| stage | ||
| t | ||
| n | ||
| m | ||
| -historic | ||
| location |
| filename | section | description |
|---|---|---|
| patientId_tumor.csv | Patient_ID | |
| -record_id | ||
| location | ||
| -topography_major | ||
| -topography_minor | ||
| clockface | ||
| quadrant | ||
| laterality | ||
| -laterality_code | ||
| diagnosis | ||
| histology | ||
| -histologic_type | ||
| cancer_type | ||
| extent | ||
| -behavior | ||
| tumor_type | ||
| -tumor_size | ||
| -tumor_size_procedure | ||
| -calcifications | ||
| ER_ | ||
| -ER_amount | ||
| -ER_procedure | ||
| PR_ | ||
| -PR_amount | ||
| -PR_procedure | ||
| HER2 | ||
| -HER2_amount | ||
| -HER2_procedure | ||
| KI67 | ||
| BRCA1 | ||
| BRCA2 | ||
| ALK | ||
| EGFR | ||
| BRAF | ||
| ROS1 | ||
| PDL1 | ||
| MSI | ||
| KRAS | ||
| PSA | ||
| PSA_EL | ||
| -treatment |
PatientSummaryXnTableWriter
| filename | section | description |
|---|---|---|
| ?_cancer.csv | Patient_ID | |
| CancerId | ||
| Cancer Class & Confidence | ||
| Topography, major | ||
| Topography, minor | ||
| Laterality | ||
| Lymph Involvement | ||
| Metastatic Site | ||
| Histology | ||
| Grade | ||
| Stage | ||
| T Stage | ||
| N Stage | ||
| M Stage | ||
| Course | ||
| Test Results | ||
| Treatments | ||
| Procedures | ||
| Genes | ||
| Comorbidities |
| filename | section | description |
|---|---|---|
| ?_tumor.csv | Patient_ID | |
| CancerId | ||
| Cancer Class & Confidence | ||
| Topography, major | ||
| Topography, minor | ||
| Laterality | ||
| Clockface | ||
| Quadrant | ||
| Grade | ||
| Tissue | ||
| Behavior | ||
| Receptor Status | ||
| Test Results |
PatientSummaryXnJsonFileWriter
Configuration Options
SubDirectory=JSON
| filename | section | description |
|---|---|---|
| PatientID.json | id | The ID number of the patient. |
| name | The name of the patient. | |
| PatientID_Cancers.json | tumors | A list of tumors (identified by a conceptId) and the tumor's attributes (Location, Topography, Laterality, Behavior, etc.) |
| attributes | A list of the Cancer attributes (Grade, Stage, Treatments, Procedures, etc.) | |
| conceptIds | A list of the concepts for the cancer (e.g. the type of cancer). | |
| PatientID_Concepts.json | concepts | A list of concepts (e.g. Malignant, Lymph, Invasive) for the patient. For each concept found, the mentionID of the concept, dpheGroup (e.g Behavior, Body Part, Clinical Test Result), preferredText, CUI, confidence, and other relevant information are recorded. |
| conceptRelations | A list of how two concepts relate to each other, with an associated relation type. For example: UnifocalLesion (concept 1) hasAssociatedSite (type) RenalVein (concept 2). | |
| PatientID_NoteID_Doc.json | id, name, type, date, episode, text | Summary information for an individual report. Specifically the id of the report, the name of the report (e.g. pathology), the type (e.g. clinical note), the date, the episode (e.g. Diagnostic), and the full text of the report. |
| mentions | A list of all mentions in the report. | |
| mentionRelations | A list of all mention relations in the report. |