gab0/pmc-antibody

Introduction

PMC-AB aims to mimic CiteAB's functionaliy as an Antibody citation search engine.

Currently we search articles on EuropePMC.

This software is packaged as a Python module.

Workflow

For a given input that uniquely identifies a commercially available antibody, this program generates EuropePMC-compatible search queries that will return articles that cite that antibody.

Queries are generated by replacing previously-known templates that represent ways that a antibody can be referenced in academic texts

Input

Antibody data: SKU, CLONE_ID, MANUFACTURER, ``

Query templates

$SKU $MANUFACTURER
#$TARGET*$CLONE
#$MANUFACTURER AND $CLONE
#$SKU AND $MANUFACTURER
"$TARGET \(Clone #$CLONE, $MANUFACTURER"
"$TARGET antibody \($CLONE; $MANUFACTURER"
"$MANUFACTURER clone $CLONE"
"$MANUFACTURER, clone $CLONE"

Built queries

Applying antibody information to our query templates yield a list of independent queries:

"CD4 \(Clone #RM4-5, BD Biosciences"
"CD4 \(Clone #RM4-5, BDBiosciences"
"CD4 \(Clone #RM4-5, BD-Biosciences"
"CD4 antibody \(RM4-5; BD Biosciences"
"CD4 antibody \(RM4-5; BDBiosciences"
"CD4 antibody \(RM4-5; BD-Biosciences"
"BD Biosciences clone RM4-5"
"BDBiosciences clone RM4-5"
"BD-Biosciences clone RM4-5"
"BD Biosciences, clone RM4-5"
"BDBiosciences, clone RM4-5"
"BD-Biosciences, clone RM4-5"

We can combine independent queries with OR directives so we can query all of them in a single API call:

(550280 BD Biosciences) OR (550280 BDBiosciences) OR (550280 BD-Biosciences) OR ("CD4 \(Clone #RM4-5, BD Biosciences") OR ("CD4 \(Clone #RM4-5, BDBiosciences") OR ("CD4 \(Clone #RM4-5, BD-Biosciences") OR ("CD4 antibody \(RM4-5; BD Biosciences") OR ("CD4 antibody \(RM4-5; BDBiosciences") OR ("CD4 antibody \(RM4-5; BD-Biosciences") OR ("BD Biosciences clone RM4-5") OR ("BDBiosciences clone RM4-5") OR ("BD-Biosciences clone RM4-5") OR ("BD Biosciences, clone RM4-5") OR ("BDBiosciences, clone RM4-5") OR ("BD-Biosciences, clone RM4-5")

Validation

To validate search results, we compare to the .xlsx reference, which is based on CiteAB results.

Application execution two type of files:

1. A .csv record containing overall statistics:

Antibody ID	Fulfillment Rate	Fulfillment rate PMC	False Positive Rate	Search Hit Count	Search N	Agreement N	Benchmark N (CiteAB)
BD Biosciences:550280	63.76%	78.54%	95.13%	6952	6900	336	527
Invitrogen:11-0041-82	35.95%	39.77%	96.31%	4471	4472	165	459
Abcam:ab183685	80.71%	97.66%	16.31%	325	325	272	337
BioLegend:100401	92.47%	87.61%	94.38%	5467	5467	307	332
Abcam:ab133616	77.62%	93.33%	29.75%	316	316	222	286
R&D Systems:AF1828	66.67%	90.0%	4.76%	42	42	40	60
R&D Systems:BAF1828	71.43%	100.0%	0.0%	20	20	20	28

2. A list of articles that were retrieved by the application but were not in the .xlsx records, one per antibody.

Usage

Setup

Usual Python package setup:

pip install -r requirements.txt
pip install .

Execution

To evaluate all antibody records and produce result records. Files will be created in the current directory, which can be any.

pmcab -a