NCI DTP Molecular Target Query Skill
Search NCI-60 protein-level molecular target data by any entity. Auto-detects type:
| Input Pattern |
Detected As |
Match Logic |
EGFR, TP53 |
gene / protein |
exact on GENE or substring on ENTITY_MEASURED, TITLE |
MCF7, NCI-H460 |
cell line |
substring on cellname |
Breast, Leukemia |
cancer panel |
substring on pname |
12345 (pure digits) |
MOLTID |
exact on MOLTID (NCI pattern #) |
Drug-Relevance Guide
Only protein expression data is downloaded — proteins are the direct molecular
targets of drugs (kinase inhibitors → kinase expression, antibodies → receptor levels).
| Dataset |
Download? |
Reason |
| WEB_DATA_PROTEIN.ZIP |
YES |
Drug targets: protein expression across NCI-60 |
| WEB_DATA_ALL_MT.ZIP |
Optional |
Superset incl. enzyme activity (also drug-relevant) |
| WEB_DATA_DNA.ZIP |
No |
Genomic characterisation, not drug targets |
| WEB_DATA_SEQUENOM_METHYLATION.ZIP |
No |
Epigenetic; indirect |
| WEB_DATA_*_MIR.ZIP |
No |
microRNA regulation; indirect |
| WEB_DATA_METABOLON*.ZIP |
No |
Metabolomics; downstream, indirect |
| Microarray / SNP / CopyNum / Karyotype |
No |
Cell-line genomic profiling; indirect |
API
| Function |
Input |
Returns |
load_data(path) |
file or directory path |
list[dict] |
search(data, entity) |
data + single entity string |
list[dict] |
search_batch(data, entities) |
data + list of entity strings |
dict[str, list[dict]] |
summarize(hits, entity) |
hit list + label |
compact LLM-readable text |
to_json(hits) |
hit list |
list[dict] (JSON-serialisable) |
query(data, entities, top_n) |
data + str or list |
text block |
Record Fields
Each record contains:
| Field |
Description |
MOLTID |
NCI pattern number (molecular target ID) |
GENE |
Gene symbol |
TITLE |
Gene / protein full name |
MOLTNBR |
NCI experiment ID |
PANELNBR / CELLNBR |
Internal panel / cell identifiers |
pname |
Cancer panel name (e.g., Breast, Leukemia) |
cellname |
Cell line name (e.g., MCF7, A549/ATCC) |
ENTITY_MEASURED |
What was measured (e.g., protein name) |
GeneID |
NCBI Gene ID |
UNITS |
Measurement units |
METHOD |
Assay method |
VALUE |
Numeric measurement value |
TEXT |
Additional notes |
Usage
See if __name__ == "__main__" block in 16_NCI_DTP_MolTarget.py for runnable
examples covering: single gene query, cell line profile, batch multi-target
search, cancer panel query, and JSON output.
Quick Examples
from importlib.machinery import SourceFileLoader
mt = SourceFileLoader("mt", "16_NCI_DTP_MolTarget.py").load_module()
data = mt.load_data()
# Single drug target
print(mt.query(data, "EGFR"))
# Multiple targets
print(mt.query(data, ["TP53", "BRAF", "HER2"]))
# Cell line molecular profile
print(mt.query(data, "MCF7"))
# JSON for downstream pipeline
import json
hits = mt.search(data, "EGFR")
print(json.dumps(mt.to_json(hits[:5]), indent=2))
Data Source & Download
Download Commands
# File already at:
# resources_metadata/dti/Molecular Target Data/WEB_DATA_PROTEIN.TXT
1---2name: nci-dtp-moltarget3description: Query the NCI-60 Molecular Target (Protein) database from the Developmental Therapeutics Program. Use when the user asks about protein expression of drug targets across the NCI-60 cancer cell line panel, or wants to look up a gene, cell line, or cancer panel in the NCI DTP molecular target dataset.4---5
6# NCI DTP Molecular Target Query Skill
7
8Search NCI-60 protein-level molecular target data by any entity. Auto-detects type:
9
10| Input Pattern | Detected As | Match Logic |
11|---|---|---|
12| `EGFR`, `TP53` | gene / protein | exact on `GENE` or substring on `ENTITY_MEASURED`, `TITLE` |
13| `MCF7`, `NCI-H460` | cell line | substring on `cellname` |
14| `Breast`, `Leukemia` | cancer panel | substring on `pname` |
15| `12345` (pure digits) | MOLTID | exact on `MOLTID` (NCI pattern #) |
16
17## Drug-Relevance Guide
18
19Only **protein expression data** is downloaded — proteins are the direct molecular
20targets of drugs (kinase inhibitors → kinase expression, antibodies → receptor levels).
21
22| Dataset | Download? | Reason |
23|---|---|---|
24| **WEB_DATA_PROTEIN.ZIP** | **YES** | Drug targets: protein expression across NCI-60 |
25| WEB_DATA_ALL_MT.ZIP | Optional | Superset incl. enzyme activity (also drug-relevant) |
26| WEB_DATA_DNA.ZIP | No | Genomic characterisation, not drug targets |
27| WEB_DATA_SEQUENOM_METHYLATION.ZIP | No | Epigenetic; indirect |
28| WEB_DATA_*_MIR.ZIP | No | microRNA regulation; indirect |
29| WEB_DATA_METABOLON*.ZIP | No | Metabolomics; downstream, indirect |
30| Microarray / SNP / CopyNum / Karyotype | No | Cell-line genomic profiling; indirect |
31
32## API
33
34| Function | Input | Returns |
35|---|---|---|
36| `load_data(path)` | file or directory path | `list[dict]` |
37| `search(data, entity)` | data + single entity string | `list[dict]` |
38| `search_batch(data, entities)` | data + list of entity strings | `dict[str, list[dict]]` |
39| `summarize(hits, entity)` | hit list + label | compact LLM-readable text |
40| `to_json(hits)` | hit list | `list[dict]` (JSON-serialisable) |
41| `query(data, entities, top_n)` | data + str or list | text block |
42
43## Record Fields
44
45Each record contains:
46
47| Field | Description |
48|---|---|
49| `MOLTID` | NCI pattern number (molecular target ID) |
50| `GENE` | Gene symbol |
51| `TITLE` | Gene / protein full name |
52| `MOLTNBR` | NCI experiment ID |
53| `PANELNBR` / `CELLNBR` | Internal panel / cell identifiers |
54| `pname` | Cancer panel name (e.g., Breast, Leukemia) |
55| `cellname` | Cell line name (e.g., MCF7, A549/ATCC) |
56| `ENTITY_MEASURED` | What was measured (e.g., protein name) |
57| `GeneID` | NCBI Gene ID |
58| `UNITS` | Measurement units |
59| `METHOD` | Assay method |
60| `VALUE` | Numeric measurement value |
61| `TEXT` | Additional notes |
62
63## Usage
64
65See `if __name__ == "__main__"` block in `16_NCI_DTP_MolTarget.py` for runnable
66examples covering: single gene query, cell line profile, batch multi-target
67search, cancer panel query, and JSON output.
68
69## Quick Examples
70
71```python
72from importlib.machinery import SourceFileLoader
73mt = SourceFileLoader("mt", "16_NCI_DTP_MolTarget.py").load_module()
74
75data = mt.load_data()
76
77# Single drug target
78print(mt.query(data, "EGFR"))
79
80# Multiple targets
81print(mt.query(data, ["TP53", "BRAF", "HER2"]))
82
83# Cell line molecular profile
84print(mt.query(data, "MCF7"))
85
86# JSON for downstream pipeline
87import json
88hits = mt.search(data, "EGFR")
89print(json.dumps(mt.to_json(hits[:5]), indent=2))
90```
91
92## Data Source & Download
93
94- **Provider**: NCI Developmental Therapeutics Program (DTP)
95- **URL**: https://wiki.nci.nih.gov/spaces/NCIDTPdata/pages/155845004/Molecular+Target+Data
96- **File**: `WEB_DATA_PROTEIN.TXT` (headerless CSV, comma-delimited)
97- **Local Path**: `resources_metadata/dti/Molecular Target Data/WEB_DATA_PROTEIN.TXT`
98- **Format**: comma-delimited, 14 columns (see Record Fields above)
99- **Auth**: None (public domain, U.S. government)
100
101### Download Commands
102
103```bash
104# File already at:
105# resources_metadata/dti/Molecular Target Data/WEB_DATA_PROTEIN.TXT
106```
gabrielmoreira