pynidm 4.1.0

Description:

pynidm 4.1.0

1 PyNIDM: Neuroimaging Data Model in Python
A Python library to manipulate the Neuroimaging Data Model.


Contents

1 PyNIDM: Neuroimaging Data Model in Python

1.1 Dependencies
1.2 Installation
1.3 Contributing to the Software
1.4 Reporting Issues or Problems
1.5 Support and Feedback
1.6 NIDM-Experiment Tools

1.6.1 BIDS MRI Conversion to NIDM
1.6.2 CSV File to NIDM Conversion
1.6.3 convert
1.6.4 concatenate
1.6.5 visualize
1.6.6 merge
1.6.7 Query
1.6.8 linear_regression




2 PyNIDM: REST API and Command Line Usage

2.1 Introduction
2.2 Installation
2.3 URI formats

2.3.1 Operations
2.3.2 Query Parameters


2.4 Return Formatting

2.4.1 Examples

2.4.1.1 Get the UUID for all the projects at this location
2.4.1.2 Get the project summary details
2.4.1.3 Get the subjects in a project
2.4.1.4 Use the command line to get statistics on a project for the AGE_AT_SCAN and a FSL data element
2.4.1.5 Get details on a subject




2.5 Additional NIDM-related Tools





1.1 Dependencies

Git-annex
Graphviz (native package):

Fedora: dnf install graphviz
OS-X: brew install graphviz





1.2 Installation
$ pip install pynidm


1.3 Contributing to the Software
This software is open source and community developed. As such, we encourage
anyone and everyone interested in semantic web and neuroimaging to contribute.
To begin contributing code to the repository, please fork the main repo into
your user space and use the pull request GitHub feature to submit code for
review. Please provide a reasonably detailed description of what was changed
and why in the pull request.


1.4 Reporting Issues or Problems
If you encounter a bug, you can directly report it in the issues section.
Please describe how to reproduce the issue and include as much information as
possible that can be helpful for fixing it. If you would like to suggest a fix,
please open a new pull request or include your suggested fix in the issue.


1.5 Support and Feedback
We would love to hear your thoughts on our Python toolbox. Feedback, questions,
or feature requests can also be submitted as issues. Note, we are a small band
of researchers who mostly volunteer our time to this project. We will respond
as quickly as possible.


1.6 NIDM-Experiment Tools

1.6.1 BIDS MRI Conversion to NIDM
This program will convert a BIDS MRI dataset to a NIDM-Experiment RDF document.
It will parse phenotype information and simply store variables/values and link
to the associated json data dictionary file. To use this tool please set your
INTERLEX_API_KEY environment variable to your unique API key. To get an
Interlex API key you visit SciCrunch,
register for an account, then click on “MyAccount” and “API Keys” to add a new
API key for your account.
$ bidsmri2nidm -d [ROOT BIDS DIRECT] -bidsignore

usage: bidsmri2nidm [-h] -d DIRECTORY [-jsonld] [-bidsignore] [-no_concepts]
[-json_map JSON_MAP] [-log LOGFILE] [-o OUTPUTFILE]

This program will represent a BIDS MRI dataset as a NIDM RDF document and provide user with opportunity to annotate
the dataset (i.e. create sidecar files) and associate selected variables with broader concepts to make datasets more
FAIR.

Note, you must obtain an API key to Interlex by signing up for an account at scicrunch.org then going to My Account
and API Keys. Then set the environment variable INTERLEX_API_KEY with your key.

optional arguments:
-h, --help show this help message and exit
-d DIRECTORY Full path to BIDS dataset directory
-jsonld, --jsonld If flag set, output is json-ld not TURTLE
-bidsignore, --bidsignore
If flag set, tool will add NIDM-related files to .bidsignore file
-no_concepts, --no_concepts
If flag set, tool will no do concept mapping
-log LOGFILE, --log LOGFILE
Full path to directory to save log file. Log file name is bidsmri2nidm_[basename(args.directory)].log
-o OUTPUTFILE Outputs turtle file called nidm.ttl in BIDS directory by default..or whatever path/filename is set here

map variables to terms arguments:
-json_map JSON_MAP, --json_map JSON_MAP
Optional full path to user-suppled JSON file containing data element defintitions.


1.6.2 CSV File to NIDM Conversion
This program will load in a CSV file and iterate over the header variable names
performing an elastic search of https://scicrunch.org/nidm-terms for
NIDM-ReproNim tagged terms that fuzzy match the variable names. The user will
then interactively pick a term to associate with the variable name. The
resulting annotated CSV data will then be written to a NIDM data file. To use
this tool please set your INTERLEX_API_KEY environment variable to your unique
API key. To get an Interlex API key you visit SciCrunch, register for an account, then click on
“MyAccount” and “API Keys” to add a new API key for your account.
usage: csv2nidm [-h] -csv CSV_FILE [-json_map JSON_MAP | -redcap REDCAP]
[-nidm NIDM_FILE] [-no_concepts] [-log LOGFILE] -out
OUTPUT_FILE

This program will load in a CSV file and iterate over the header variable
names performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim
tagged terms that fuzzy match the variable names. The user will then
interactively pick a term to associate with the variable name. The resulting
annotated CSV data will then be written to a NIDM data file. Note, you must
obtain an API key to Interlex by signing up for an account at scicrunch.org
then going to My Account and API Keys. Then set the environment variable
INTERLEX_API_KEY with your key. The tool supports import of RedCap data
dictionaries and will convert relevant information into a json-formatted
annotation file used to annotate the data elements in the resulting NIDM file.

optional arguments:
-h, --help show this help message and exit
-csv CSV_FILE Full path to CSV file to convert
-json_map JSON_MAP Full path to user-suppled JSON file containing
variable-term mappings.
-redcap REDCAP Full path to a user-supplied RedCap formatted data
dictionary for csv file.
-nidm NIDM_FILE Optional full path of NIDM file to add CSV->NIDM
converted graph to
-no_concepts If this flag is set then no concept associations will
beasked of the user. This is useful if you already
have a -json_map specified without concepts and want
tosimply run this program to get a NIDM file with user
interaction to associate concepts.
-log LOGFILE, --log LOGFILE
full path to directory to save log file. Log file name
is csv2nidm_[arg.csv_file].log
-out OUTPUT_FILE Full path with filename to save NIDM file


1.6.3 convert
This function will convert NIDM files to various RDF-supported formats and name
then / put them in the same place as the input file.
Usage: pynidm convert [OPTIONS]

Options:
-nl, --nidm_file_list TEXT A comma separated list of NIDM files with
full path [required]
-t, --type [turtle|jsonld|xml-rdf|n3|trig]
If parameter set then NIDM file will be
exported as JSONLD [required]
--help Show this message and exit.


1.6.4 concatenate
This function will concatenate NIDM files. Warning, no merging will be done so
you may end up with multiple prov:agents with the same subject id if you’re
concatenating NIDM files from multiple visits of the same study. If you want
to merge NIDM files on subject ID see pynidm merge
Usage: pynidm concat [OPTIONS]

Options:
-nl, --nidm_file_list TEXT A comma separated list of NIDM files with full
path [required]
-o, --out_file TEXT File to write concatenated NIDM files
[required]
--help Show this message and exit.


1.6.5 visualize
This command will produce a visualization(pdf) of the supplied NIDM files named
the same as the input files and stored in the same directories.
Usage: pynidm visualize [OPTIONS]

Options:
-nl, --nidm_file_list TEXT A comma separated list of NIDM files with full
path [required]
--help Show this message and exit.


1.6.6 merge
This function will merge NIDM files. See command line parameters for supported
merge operations.
Usage: pynidm merge [OPTIONS]

Options:
-nl, --nidm_file_list TEXT A comma separated list of NIDM files with full
path [required]
-s, --s If parameter set then files will be merged by
ndar:src_subjec_id of prov:agents
-o, --out_file TEXT File to write concatenated NIDM files
[required]
--help Show this message and exit.


1.6.7 Query
This function provides query support for NIDM graphs.
Usage: pynidm query [OPTIONS]

Options:
-nl, --nidm_file_list TEXT A comma separated list of NIDM files with
full path [required]
-nc, --cde_file_list TEXT A comma separated list of NIDM CDE files
with full path. Can also be set in the
CDE_DIR environment variable
-q, --query_file FILENAME Text file containing a SPARQL query to
execute
-p, --get_participants Parameter, if set, query will return
participant IDs and prov:agent entity IDs
-i, --get_instruments Parameter, if set, query will return list of
onli:assessment-instrument:
-iv, --get_instrument_vars Parameter, if set, query will return list of
onli:assessment-instrument: variables
-de, --get_dataelements Parameter, if set, will return all
DataElements in NIDM file
-debv, --get_dataelements_brainvols
Parameter, if set, will return all brain
volume DataElements in NIDM file along with
details
-bv, --get_brainvols Parameter, if set, will return all brain
volume data elements and values along with
participant IDs in NIDM file
-o, --output_file TEXT Optional output file (CSV) to store results
of query
-u, --uri TEXT A REST API URI query
-j / -no_j Return result of a uri query as JSON
-v, --verbosity TEXT Verbosity level 0-5, 0 is default
--help Show this message and exit.
Details on the REST API URI format and usage can be found on the REST API usage
page.


1.6.8 linear_regression
This function provides linear regression support for NIDM graphs.
Usage: pynidm linear-regression [OPTIONS]

Options:
-nl, --nidm_file_list TEXT A comma-separated list of NIDM files with
full path [required]
-r, --regularization TEXT Parameter, if set, will return the results of
the linear regression with L1 or L2 regularization
depending on the type specified, and the weight
with the maximum likelihood solution. This will
prevent overfitting. (Ex: -r L1)
-model, --ml TEXT An equation representing the linear
regression. The dependent variable comes
first, followed by "=" or "~", followed by
the independent variables separated by "+"
(Ex: -model "fs_003343 = age*sex + sex +
age + group + age*group + bmi") [required]
-contstant, --ctr TEXT Parameter, if set, will return differences in
variable relationships by group. One or
multiple parameters can be used (multiple
parameters should be separated by a comma-
separated list) (Ex: -contrast group,age)
-o, --output_file TEXT Optional output file (TXT) to store results
of query
--help Show this message and exit.
To use the linear regression algorithm successfully, structure, syntax, and
querying is important. Here is how to maximize the usefulness of the tool:
First, use pynidm query to discover the variables to use. PyNIDM allows for the
use of either data elements (PIQ_tca9ck), specific URLs
(http://uri.interlex.org/ilx_0100400), or source variables (DX_GROUP).
An example of a potential query is:
pynidm query -nl /simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl,/simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_b/nidm.ttl -u /projects?fields=fs_000008,DX_GROUP,PIQ_tca9ck,http://uri.interlex.org/ilx_0100400
You can also do:
pynidm query -nl /simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl,/Users/Ashu/Downloads/simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_b/nidm.ttl -gf fs_000008,DX_GROUP,PIQ_tca9ck,http://uri.interlex.org/ilx_0100400
The query looks in the two files specified in the -nl parameter for the
variables specified. In this case, we use fs_000008 and DX_GROUP (source
variables), a URL (http://uri.interlex.org/ilx_0100400), and a data element
(PIQ_tca9ck). The output of the file is slightly different depending on whether
you use -gf or -u. With -gf, it will return the variables from both files
separately, while -u combines them.
Now that we have selected the variables, we can perform a linear regression. In
this example, we will look at the effect of DX_GROUP, age at scan, and PIQ on
supratentorial brain volume.
The command to use for this particular data is:
pynidm linear-regression -nl /simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl,/simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_b/nidm.ttl -model "fs_000008 = DX_GROUP + PIQ_tca9ck + http://uri.interlex.org/ilx_0100400" -contrast "DX_GROUP" -r L1
-nl specifies the file(s) to pull data from, while -model is the model to
perform a linear regression model on. In this case, the variables are fs_000008
(the dependent variable, supratentorial brain volume), DX_GROUP (diagnostic
group), PIQ_tca9ck (PIQ), and http://uri.interlex.org/ilx_0100400 (age at
scan). The -contrast parameter says to contrast the data using DX_GROUP, and
then do a L1 regularization to prevent overfitting.
Details on the REST API URI format and usage can be found below.




2 PyNIDM: REST API and Command Line Usage

2.1 Introduction
There are two main ways to interact with NIDM data using the PyNIDM REST API.
First, the pynidm query command line utility will accept queries formatted as
REST API URIs. Second, the rest-server.py script can be used to run a HTTP
server to accept and process requests. This script can either be run directly
or using a docker container defined in the docker directory of the project.
Example usage:
$ pynidm query -nl "cmu_a.ttl,cmu_b.ttl" -u /projects

dc1bf9be-10a3-11ea-8779-003ee1ce9545
ebe112da-10a3-11ea-af83-003ee1ce9545


2.2 Installation
To use the REST API query syntax on the command line, follow the PyNIDM
installation instructions.
The simplest way to deploy a HTTP REST API server would be with the provided
docker container. You can find instructions for that process in the README.md file in the docker
directory of the Github repository.


2.3 URI formats
You can find details on the REST API at the SwaggerHub API Documentation. The OpenAPI
specification file is part of the Github repository in
‘docs/REST_API_definition.openapi.yaml’
Here is a list of the current operations. See the SwaggerHub page for more
details and return formats.
- /projects
- /projects/{project_id}
- /projects/{project_id}/subjects
- /projects/{project_id}/subjects?filter=[filter expression]
- /projects/{project_id}/subjects/{subject_id}
- /projects/{project_id}/subjects/{subject_id}/instruments/{instrument_id}
- /projects/{project_id}/subjects/{subject_id}/derivatives/{derivative_id}
- /statistics/projects/{project_id}
You can append the following query parameters to many of the operations:
- filter
- field

2.3.1 Operations

/projects
Get a list of all project IDs available.
Supported query parameters: none

/projects/{project_id}
See some details for a project. This will include the list of subject IDs
and data elements used in the project
Supported query parameters: filter

/projects/{project_id}/subjects
Get the list of subjects in a project
Supported query parameters: filter

/projects/{project_id}/subjects/{subject_id}
Get the details for a particular subject. This will include the results of
any instrumnts or derivatives associated with the subject, as well as a
list of the related activities.
Supported query parameters: none

/projects/{project_id}/subjects/{subject_id}/instruments/{instrument_id}
Get the values for a particular instrument
Supported query parameters: none

/projects/{project_id}/subjects/{subject_id}/derivatives/{derivative_id}
Get the values for a particular derivative
Supported query parameters: none

/statistics/projects/{project_id}
See project statistics. You can also use this operation to get statsitcs on
a particular instrument or derivative entry by use a field query option.
Supported query parameters: filter, field

/statistics/projects/{project_id}/subjects/{subject_id}
See some details for a project. This will include the list of subject IDs
and data elements used in the project
Supported query parameters: none




2.3.2 Query Parameters

filter
The filter query parameter is used when you want to receive data only on
subjects that match some criteria. The format for the filter value should
be of the form:
identifier op value [ and identifier op value and ... ]
Identifiers should be formatted as “instrument.ID” or “derivatives.ID” You
can use any value for the instrument ID that is shown for an instrument or
in the data_elements section of the project details. For the derivative ID,
you can use the last component of a derivative field URI (ex. for the URI
http://purl.org/nidash/fsl#fsl_000007, the ID would be “fsl_000007”) or the
exact label shown when viewing derivative data (ex. “Left-Caudate (mm^3)”).
The op can be one of “eq”, “gt”, “lt”.

Example filters:
?filter=instruments.AGE_AT_SCAN gt 30
?filter=instrument.AGE_AT_SCAN eq 21 and derivative.fsl_000007 lt 3500



fields
The fields query parameter is used to specify what fields should be
detailed in a statistics operation. For each field specified the result
will show minimum, maximum, average, median, and standard deviation for the
values of that field across all subjects matching the operation and filter.
Multiple fields can be specified by separating each field with a comma.
Fields should be formatted in the same way as identifiers are specified in
the filter parameter.

Example field query:
http://localhost:5000/statistics/projects/abc123?field=instruments.AGE_AT_SCAN,derivatives.fsl_000020







2.4 Return Formatting
By default the HTTP REST API server will return JSON formatted objects or
arrays. When using the pynidm query command line utility the default return
format is text (when possible) or you can use the -j option to have the output
formatted as JSON.

2.4.1 Examples

2.4.1.1 Get the UUID for all the projects at this location
curl http://localhost:5000/projects
Example response:
[
"dc1bf9be-10a3-11ea-8779-003ee1ce9545"
]


2.4.1.2 Get the project summary details
curl http://localhost:5000/projects/dc1bf9be-10a3-11ea-8779-003ee1ce9545
Example response:
{
"http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "http://purl.org/nidash/nidm#Project",
"dctypes:title": "ABIDE CMU_a Site",
"http://www.w3.org/ns/prov#Location": "/datasets.datalad.org/abide/RawDataBIDS/CMU_a",
"sio:Identifier": "1.0.1",
"nidm:NIDM_0000171": 14,
"age_max": 33.0,
"age_min": 21.0,
"ndar:gender": [
"1",
"2"
],
"obo:handedness": [
"R",
"L",
"Ambi"
]
}


2.4.1.3 Get the subjects in a project
pynidm query -nl "cmu_a.nidm.ttl" -u http://localhost:5000/projects/dc1bf9be-10a3-11ea-8779-003ee1ce9545/subjects
Example response:
deef8eb2-10a3-11ea-8779-003ee1ce9545
df533e6c-10a3-11ea-8779-003ee1ce9545
ddbfb454-10a3-11ea-8779-003ee1ce9545
df21cada-10a3-11ea-8779-003ee1ce9545
dcfa35b2-10a3-11ea-8779-003ee1ce9545
de89ce4c-10a3-11ea-8779-003ee1ce9545
dd2ce75a-10a3-11ea-8779-003ee1ce9545
ddf21020-10a3-11ea-8779-003ee1ce9545
debc0f74-10a3-11ea-8779-003ee1ce9545
de245134-10a3-11ea-8779-003ee1ce9545
dd5f2f30-10a3-11ea-8779-003ee1ce9545
dd8d4faa-10a3-11ea-8779-003ee1ce9545
df87cbaa-10a3-11ea-8779-003ee1ce9545
de55285e-10a3-11ea-8779-003ee1ce9545


2.4.1.4 Use the command line to get statistics on a project for the AGE_AT_SCAN and a FSL data element
pynidm query -nl ttl/cmu_a.nidm.ttl -u /statistics/projects/dc1bf9be-10a3-11ea-8779-003ee1ce9545?fields=instruments.AGE_AT_SCAN,derivatives.fsl_000001
Example response:
------------------------------------------------- ---------------------------------------------
"http://www.w3.org/1999/02/22-rdf-syntax-ns#type" http://www.w3.org/ns/prov#Activity
"title" ABIDE CMU_a Site
"Identifier" 1.0.1
"prov:Location" /datasets.datalad.org/abide/RawDataBIDS/CMU_a
"NIDM_0000171" 14
"age_max" 33.0
"age_min" 21.0

gender
--------
1
2

handedness
------------
R
L
Ambi

subjects
------------------------------------
de89ce4c-10a3-11ea-8779-003ee1ce9545
deef8eb2-10a3-11ea-8779-003ee1ce9545
dd8d4faa-10a3-11ea-8779-003ee1ce9545
ddbfb454-10a3-11ea-8779-003ee1ce9545
de245134-10a3-11ea-8779-003ee1ce9545
debc0f74-10a3-11ea-8779-003ee1ce9545
dd5f2f30-10a3-11ea-8779-003ee1ce9545
ddf21020-10a3-11ea-8779-003ee1ce9545
dcfa35b2-10a3-11ea-8779-003ee1ce9545
df21cada-10a3-11ea-8779-003ee1ce9545
df533e6c-10a3-11ea-8779-003ee1ce9545
de55285e-10a3-11ea-8779-003ee1ce9545
df87cbaa-10a3-11ea-8779-003ee1ce9545
dd2ce75a-10a3-11ea-8779-003ee1ce9545

----------- ------------------ --------
AGE_AT_SCAN max 33
AGE_AT_SCAN min 21
AGE_AT_SCAN median 26
AGE_AT_SCAN mean 26.2857
AGE_AT_SCAN standard_deviation 4.14778
----------- ------------------ --------

---------- ------------------ -----------
fsl_000001 max 1.14899e+07
fsl_000001 min 5.5193e+06
fsl_000001 median 7.66115e+06
fsl_000001 mean 8.97177e+06
fsl_000001 standard_deviation 2.22465e+06
---------- ------------------ -----------


2.4.1.5 Get details on a subject
Use -j for a JSON-formatted response
pynidm query -j -nl "cmu_a.nidm.ttl" -u http://localhost:5000/projects/dc1bf9be-10a3-11ea-8779-003ee1ce9545/subjects/df21cada-10a3-11ea-8779-003ee1ce9545
Example response:
{
"uuid": "df21cada-10a3-11ea-8779-003ee1ce9545",
"id": "0050665",
"activity": [
"e28dc764-10a3-11ea-a7d3-003ee1ce9545",
"df28e95a-10a3-11ea-8779-003ee1ce9545",
"df21c76a-10a3-11ea-8779-003ee1ce9545"
],
"instruments": {
"e28dd218-10a3-11ea-a7d3-003ee1ce9545": {
"SRS_VERSION": "nan",
"ADOS_MODULE": "nan",
"WISC_IV_VCI": "nan",
"WISC_IV_PSI": "nan",
"ADOS_GOTHAM_SOCAFFECT": "nan",
"VINELAND_PLAY_V_SCALED": "nan",
"null": "http://www.w3.org/ns/prov#Entity",
"VINELAND_EXPRESSIVE_V_SCALED": "nan",
"SCQ_TOTAL": "nan",
"SRS_MOTIVATION": "nan",
"PIQ": "104.0",
"FIQ": "109.0",
"WISC_IV_PRI": "nan",
"FILE_ID": "CMU_a_0050665",
"VIQ": "111.0",
"WISC_IV_VOCAB_SCALED": "nan",
"VINELAND_DAILYLVNG_STANDARD": "nan",
"WISC_IV_SIM_SCALED": "nan",
"WISC_IV_DIGIT_SPAN_SCALED": "nan",
"AGE_AT_SCAN": "33.0"
}
},
"derivatives": {
"b9fe0398-16cc-11ea-8729-003ee1ce9545": {
"URI": "http://iri.nidash.org/b9fe0398-16cc-11ea-8729-003ee1ce9545",
"values": {
"http://purl.org/nidash/fsl#fsl_000005": {
"datumType": "ilx_0102597",
"label": "Left-Amygdala (voxels)",
"value": "1573",
"units": "voxel"
},
"http://purl.org/nidash/fsl#fsl_000004": {
"datumType": "ilx_0738276",
"label": "Left-Accumbens-area (mm^3)",
"value": "466.0",
"units": "mm^3"
},
"http://purl.org/nidash/fsl#fsl_000003": {
"datumType": "ilx_0102597",
"label": "Left-Accumbens-area (voxels)",
"value": "466",
"units": "voxel"
}
},
"StatCollectionType": "FSLStatsCollection"
}
}




2.5 Additional NIDM-related Tools

NIDM-Terms <https://github.com/NIDM-Terms/terms>
NIDM-Terms Scicrunch Interface <https://scicrunch.org/nidm-terms>
Freesurfer stats -> NIDM <https://github.com/repronim/segstats_jsonld>
FSL structural segmentation -> NIDM <https://github.com/ReproNim/fsl_seg_to_nidm>
ANTS structural segmentation -> NIDM <https://github.com/ReproNim/ants_seg_to_nidm>