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https://github.com/hscells/transmute
PubMed/Medline query transpiler
https://github.com/hscells/transmute
medline medline-parser pubmed pubmed-parser systematic-reviews
Last synced: about 2 months ago
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PubMed/Medline query transpiler
- Host: GitHub
- URL: https://github.com/hscells/transmute
- Owner: hscells
- License: mit
- Created: 2017-06-05T05:46:12.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-12-26T01:16:56.000Z (almost 5 years ago)
- Last Synced: 2024-06-19T09:13:11.879Z (6 months ago)
- Topics: medline, medline-parser, pubmed, pubmed-parser, systematic-reviews
- Language: Go
- Homepage: https://godoc.org/github.com/hscells/transmute
- Size: 816 KB
- Stars: 7
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# transmute
[](https://godoc.org/github.com/hscells/transmute)
[](https://goreportcard.com/report/github.com/hscells/transmute)
[](https://gocover.io/github.com/hscells/transmute)
_PubMed/Medline Query Transpiler_
The goal of transmute is to provide a way of transforming PubMed/Medline search strategies from systematic reviews into
other queries suitable for other search engines. The result of the transformation is an _immediate representation_ which
can be analysed with greater ease or transformed again run on other search engines. This is why transmute is described
as a _transpiler_. An immediate representation allows trivial transformation to boolean queries acceptable by search
engines, such as Elasticsearch.
An example of a Medline and Pubmed query are:
```
1. MMSE*.ti,ab.
2. sMMSE.ti,ab.
3. Folstein*.ti,ab.
4. MiniMental.ti,ab.
5. \"mini mental stat*\".ti,ab.
6. or/1-5
```
```
(\"Contraceptive Agents, Female\"[Mesh] OR \"Contraceptive Devices, Female\"[Mesh] OR contracept*[tiab]) AND (\"Body Weight\"[Mesh] OR weight[tiab] OR \"Body Mass Index\"[Mesh]) NOT (cancer*[ti] OR polycystic [ti] OR exercise [ti] OR physical activity[ti] OR postmenopaus*[ti])
```
Both are valid Pubmed and Medline search strategies reported in real systematic reviews; transmute can currently
transform both Medline and PubMed queries. An example API usage by constructing a pipeline and executing it is shown in
the next section.
## API Usage
Here we construct a pipeline in Go:
```go
query := `1. MMSE*.ti,ab.
2. sMMSE.ti,ab.
3. Folstein*.ti,ab.
4. MiniMental.ti,ab.
5. \"mini mental stat*\".ti,ab.
6. or/1-5`
p := transmute.pipeline.NewPipeline(transmute.parser.NewMedlineParser(),
transmute.backend.NewElasticsearchCompiler(),
transmute.pipeline.TransmutePipelineOptions{RequiresLexing: true})
dsl, err := p.Execute(query)
if err != nil {
panic(err)
}
println(dsl.StringPretty())
```
Which results in:
```json
{
"query": {
"bool": {
"disable_coord": true,
"should": [
{
"bool": {
"should": [
{
"wildcard": {
"title": "MMSE*"
}
},
{
"wildcard": {
"abstract": "MMSE*"
}
}
]
}
},
{
"multi_match": {
"fields": [
"title",
"abstract"
],
"query": "sMMSE"
}
},
{
"bool": {
"should": [
{
"wildcard": {
"title": "Folstein*"
}
},
{
"wildcard": {
"abstract": "Folstein*"
}
}
]
}
},
{
"multi_match": {
"fields": [
"title",
"abstract"
],
"query": "MiniMental"
}
},
{
"bool": {
"should": [
{
"wildcard": {
"title": "\"mini mental stat*\""
}
},
{
"wildcard": {
"abstract": "\"mini mental stat*\""
}
}
]
}
}
]
}
}
}
```
## Command Line Usage
As well as being a well-documented library, transmute can also be used on the command line. Since it is still in
development, it can be built from source with go tools:
```bash
go get -u github.com/hscells/transmute/cmd/transmute
transmute --help
transmute --input mmse.query --parser medline --backend elasticsearch
```
The output of the command line pretty-prints the same output from above.
## Assumptions
The goal of transmute is to parse and transform PubMed/Medline queries into queries suitable for other search engines.
However, the project makes some assumptions about the query:
- The parser does not attempt to simplify boolean expressions, so badly written queries will remain inefficient.
- A query cannot compile to Elasticsearch when it contains an adjacency operator with more than one field. This is
due to a limitation with Elasticsearch.
## Extending
If you would like to extend transmute and create a new backend for it, have a read of the
[documentation](https://godoc.org/github.com/hscells/transmute/backend#Backend). As this should lead you in the right
direction. Writing a new backend requires the transformation of the immediate representation into the target query
language.
## Citing
If you use this work for scientific publication, please reference
```
@inproceedings{scells2018framework,
author = {Scells, Harrisen and Locke, Daniel and Zuccon, Guido},
title = {An Information Retrieval Experiment Framework for Domain Specific Applications},
booktitle = {The 41st International ACM SIGIR Conference on Research \& Development in Information Retrieval},
series = {SIGIR '18},
year = {2018},
}
```
## Logo
The Go gopher was created by [Renee French](https://reneefrench.blogspot.com/), licensed under
[Creative Commons 3.0 Attributions license](https://creativecommons.org/licenses/by/3.0/).