Validate RDF data, report problems, and support creation of more accurate data
Project description
rdf-doctor
Motivation
DBCLS has conducted to convert various life science databases to RDF and support it. This development will enable us to provide a high-quality dataset that better links existing RDF datasets stored in the RDF portal site and newly developed RDF.
Requirements
(1) Operating system
Linux (CentOS 7 or later or Ubuntu 20.04 or later), macOS 12 Monterey or later
(2) Software development language
Python
(3) Operating system environment
Main memory: 32 GB or less
Hard disk: 2TB or less
Install
pip install rdf-doctor
Command Line Interface
$ rdf-doctor --help
usage: rdf-doctor -i RDF-FILE [Options]
Home page: https://github.com/dbcls/rdf-doctor
options:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-e, --verbose show progress while processing
-i RDF-FILE [RDF-FILE ...], --input RDF-FILE [RDF-FILE ...]
input RDF file(s)(.ttl or .nt or gzip-compressed versions of them). Use the same extension when specifying multiple.
-r REPORT-FORMAT, --report REPORT-FORMAT
set the output format/serializer of report to one of: shex (defalut) or md or markdown(same as md)
-o FILE, --output FILE
write to file instead of stdout
-c URL [URL ...], --classes URL [URL ...]
set the target classes to be inspected to one of: all (defalut) or URL1, URL2,...
-p FILE, --prefix-dict FILE
path to a tab delimited file listing incorrect and correct URI pairs for the prefix (default: predefined file in rdf-doctor)
-l FILE, --class-dict FILE
path to a tab delimited file listing incorrect and correct URI pairs for the class (default: predefined file in rdf-doctor)
-f INPUT-FORMAT, --force-format INPUT-FORMAT
This option should not normally be used. Because the input format is automatically determined by the file extension. Use it only when you want to force specification. If used, "turtle" or "nt" can be specified.
See Also
- [1] https://github.com/DaniFdezAlvarez/shexer
- [2] http://shex.io/shex-primer/#combined-constraints
- [3] https://openrefine.org/docs/technical-reference/clustering-in-depth#fingerprint
Example
$ rdf-doctor -i example_1.ttl
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX oboc: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX chebi: <http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX pobo: <http://purl.obolibrary.org/obo/>
PREFIX ex: <http://example.org1/>
PREFIX ex: <http://example.org2/>
PREFIX : <http://weso.es/shapes/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xml: <http://www.w3.org/XML/1998/namespace/>
:searchId.do?chebiId=CHEBI%3ADocument [<http://purl.obolibrary.org/obo/>~] AND # 1 instance
{
rdf:type [chebi:Document] ; # 100.0 % (1 instance).
chebi:depiction xsd:string ; # 100.0 % (1 instance).
chebi:title xsd:string # 100.0 % (1 instance).
}
:searchId.do?chebiId=CHEBI%3APErson [<http://purl.obolibrary.org/obo/>~] AND # 1 instance
{
chebi:name xsd:string ; # 100.0 % (1 instance).
rdf:type [chebi:PErson] ; # 100.0 % (1 instance).
chebi:familyName xsd:string ; # 100.0 % (1 instance).
chebi:age xsd:integer # 100.0 % (1 instance).
}
:searchId.do?chebiId=CHEBI%3ADOCUMENT [<http://purl.obolibrary.org/obo/>~] AND # 1 instance
{
chebi:title xsd:string ; # 100.0 % (1 instance).
rdf:type [chebi:DOCUMENT] # 100.0 % (1 instance).
}
:searchId.do?chebiId=CHEBI%3APerson [<http://purl.obolibrary.org/obo/>~] AND # 1 instance
{
chebi:age xsd:integer ; # 100.0 % (1 instance).
chebi:name xsd:string ; # 100.0 % (1 instance).
rdf:type [chebi:Person] ; # 100.0 % (1 instance).
chebi:familyName xsd:string # 100.0 % (1 instance).
}
:searchId.do?chebiId=CHEBI%3AParson [<http://purl.obolibrary.org/obo/>~] AND # 1 instance
{
chebi:familyName xsd:string ; # 100.0 % (1 instance).
rdf:type [chebi:Parson] ; # 100.0 % (1 instance).
chebi:knows @:searchId.do?chebiId=CHEBI%3APErson ; # 100.0 % (1 instance).
chebi:name xsd:string # 100.0 % (1 instance).
}
:searchId.do?chebiId=CHEBI%3APERSON [<http://purl.obolibrary.org/obo/>~] AND # 1 instance
{
chebi:age xsd:integer ; # 100.0 % (1 instance).
chebi:name xsd:string ; # 100.0 % (1 instance).
rdf:type [chebi:PERSON] # 100.0 % (1 instance).
}
# Duplicate prefixes found.
# Input QName URI
# ex: http://example.org1/
# ex: http://example.org2/
# There may be a better QName.
# Input QName Suggested QName URI
# pobo: obo: http://purl.obolibrary.org/obo/
# pobo: uo: http://purl.obolibrary.org/obo/
$ rdf-doctor -i example_2.ttl -r md
# Report on
```
example_2.ttl
```
## Prefix reuse percentage ([?](https://github.com/dbcls/rdf-doctor#output-description))
Percentage of prefixes used in the input file that are included in the predefined prefix list inside rdf-doctor.
```
57.14%
```
## Refine prefixes ([?](https://github.com/dbcls/rdf-doctor#output-description))
Found prefixes that looks incorrect.
```
Prefix Input URI Suggested URI
chebi: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A http://purl.obolibrary.org/obo/CHEBI_
```
Duplicate prefixes found.
```
Input QName URI
ex: http://example.org1/
ex: http://example.org2/
```
## Refine classes ([?](https://github.com/dbcls/rdf-doctor#output-description))
Found class names that looks incorrect.
```
Input class name Suggested class name
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3APErson http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3APerson
```
Found multiple strings that appear to represent the same class name.
```
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3APerson
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3APErson
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3APERSON
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3ADocument
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3ADOCUMENT
```
Example of dictionary file
You can specify arbitrary dictionary files (errata) for prefixes and class URIs. It is a file in which pairs of incorrect URIs and correct URIs are tab-separated, one per line, as shown below. Specify -p , --prefix-dict for prefix, -l, --class-dict for class, followed by file. See: https://github.com/dbcls/rdf-doctor#command-line-interface
http://incorrect/uri1 http://correct/uri1
http://incorrect/uri2 http://correct/uri2
http://incorrect/uri3 http://correct/uri3
Output Description
-
Prefix reuse percentage: Percentage of prefixes used in the input file that are included in the predefined prefix list inside rdf-doctor.
-
Refine prefixes: The URI entered as a prefix is checked against a list (errata) defined inside rdf-doctor, and if there is matching information, output as correction suggestions. Also, if a prefix with the same QName but a different URI is found, it is output as a correction suggestion.
-
Refine classes: The URI of the input class is checked against the list (errata) defined inside rdf-doctor, and if there is matching information, the correct URI is suggested. Also, if the URI of the input class is converted to a key string using the fingerprinting method and multiple different strings are found even though the key strings match, they may represent the same class. Output as correction suggestions.
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