13 research outputs found
Comparing Attitudes Toward Different Consent Mediums: Semistructured Qualitative Study.
peer reviewedBACKGROUND: As consent for data sharing evolves with the digital age, plain-text consent is not the only format in which information can be presented. However, designing a good consent form is highly challenging. The addition of graphics, video, and other mediums to use can vary widely in effectiveness; and improper use can be detrimental to users.
OBJECTIVE: This study aims to explore the expectations and experiences of adults toward consent given in infographic, video, text, newsletter, and comic forms in a health data sharing scenario to better understand the appropriateness of different mediums and identify elements of each medium that most affect engagement with the content.
METHODS: We designed mock consent forms in infographic, video, text, newsletter, and comic versions. Semistructured interviews were conducted with adults who were interviewed about their expectations for consent and were then shown each consent medium and asked about engaging elements across mediums, preferences for consent mediums, and the value of document quality criteria. We transcribed and qualitatively co-coded to identify themes and perform analyses.
RESULTS: We interviewed 24 users and identified different thematic archetypes based on participant goals, such as the Trust Seeker, who considered their own understanding and trust in organizations when making decisions. The infographic was ranked first for enhancing understanding, prioritizing information, and maintaining the proper audience fit for serious consent in health data sharing scenarios. In addition, specific elements such as structure, step-by-step organization, and readability were preferred engaging elements.
CONCLUSIONS: We identified archetypes to better understand user needs and elements that can be targeted to enhance user engagement with consent forms; this can help inform the design of more effective consent in the future. Overall, preferences for mediums are highly contextual, and more research should be done
Legal-Ethical Challenges and Technological Solutions to e-Health Data Consent in the EU
e-Health data is sensitive and consenting to the collection, processing, and sharing involves compliance with legal requirements, ethical standards, and appropriate digital tools. We explore two legal-ethical challenges: 1) What are the scope and requirements of digital health data consent? 2) What are the legal-ethical reasons for obtaining consent beyond the GDPR’s legal basis, and how might such consent be obtained? We then propose human-centered solutions to help navigate standards of ethical and legal consent across the EU, purposefully addressing those use cases to compensate for human difficulties in managing consent without clear guidelines. These solutions – including ISO standards, ontologies, consent mechanisms, value-centered privacy assistants, and layered dynamic consent platforms – complement and aid humans to help uphold ethical and rigorous consent
Conciseness, interest, and unexpectedness: User attitudes towards infographic and comic consent mediums
Being asked to consent to data sharing is a ubiquitous experience in digital services - yet it is very rare to encounter a well designed consent experience. Considering the momentum and importance
of a European data space where personal information freely and easily flows across organizations, sectors and Member States, solving the long-discussed thorny issue of "how to get consent right"
cannot be postponed any further. In this paper, we describe the first findings from a study based on 24 semi-structured interviews investigating participants’ expectations and opinions toward consent in a data sharing scenario with a data trustee. We analyzed various dimensions of a consent form redesigned as a comic and an infographic, including language, information design, content and the writer-reader relationship. The results provide insights into the complexity of elements that should be considered when asking individuals to freely and mindfully disclose their data, especially sensitive information
Sage-Bionetworks/schematic: v23.9.2
What's Changed
implement GE list rule by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/655
Develop initial rule pairs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/802
Cross Manifest Validation: Value Level Comparisons and Reworked Warning Messages by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/751
Develop schema viz tool tests by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/659
make sorting case insensitive by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/830
Develop fix submit keyerror by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/831
updating the release documentation by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/817
Develop an endpoint to return data types of columns in a manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/815
Develop rule combination by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/766
BugFix: Import dataType from CLI as list not string by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/836
BugFix: Manifest Import - Mask null cells as empty strings instead of NaNs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/837
BugFix: list like behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/840
Check type of 'url' entry when raising errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/844
Fix example data model list validation rule and update "list" in ManifestGenerator to handle both list strict and list like by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/847
add warning to validate_manifest endpoint by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/859
Develop NA string behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/842
Develop blank annotation behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/862
Develop Missing Entity Handling by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/871
rename manifest based on manifest_basename when submit to synapse by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/869
Output errors generated from jsonSchema (when submitting manifest) to the console by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/873
Develop manifest submission error handle by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/879
do not create dir if located in cwd by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/881
Update annotations unit test by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/880
Develop optional rule args by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/843
Containerizing schematic (and update dependencies as needed) by @BrunoGrandePhD in https://github.com/Sage-Bionetworks/schematic/pull/882
add endpoint find_class_specific_properties by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/890
add route get_subgraph_by_edge_type by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/891
create endpoint to return schema as a pickle file by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/892
poetry documentation by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/895
Add support for Schematic API to Dockerfile by @BrunoGrandePhD in https://github.com/Sage-Bionetworks/schematic/pull/887
Create project table manifests, move entities to new project by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/829
add concurrency to github action by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/896
HOTFIX: Mixed type column manifest table upload by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/902
update asset view table endpoint to allow returning a json by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/912
added get_node_range endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/904
added get_property_label endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/905
added node_dependencies endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/906
Allow schema.org schema to be loaded and used by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/903
add example workbook to demo cli functions by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/916
change manifest name for censored manifest when upload by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/931
Add Restriction Flag to Make Synapse Table Method by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/935
Develop Table Uploads: Replace by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/917
allow users to upload csv or json file when submitting manifest using API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/908
allow users to upload csv or json file when validating manifest using API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/910
Develop table schema fix replacements by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/947
Fixing parsing of table schema parameters on table replace by @milen-sage in https://github.com/Sage-Bionetworks/schematic/pull/945
Develop schema viz tool cors by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/942
Move Schema Visualization to Schematic by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/645
add default max size for columns missing this key by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/952
populate manifest as an excel spreadsheet without sending data to Google api by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/940
Skip Trashed Entities and Entities that "do not exist" by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/985
Reword conditional requirements for the attribute table by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/987
add tests related to manifest get by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/979
fix api endpoint for docker container by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/974
Remove unused libraries by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/991
Remove Manifest Table Submission Dependency on Project Scope when not Validating by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/989
HOTFIX: Extend table replacement sleep duration to ensure synapse deletion operation completes by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/999
Pass config.yml as an environment variable to docker container by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/975
update error messages in synapseStore when manifest_basename key is missing in config.yml by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/997
Added instructions for installing and using schematic and the schematic API docker containers to README by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/953
Develop pdoc by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/957
correct typo: master_basename to manifest_basename in error message by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1005
Fixed typo in conditional requirement for schema viz attribute table by adding quotes by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1003
Added tests for all API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/995
Fixed an issue where the DCA would disconnect on manifest submission by casting UUIDs to type string by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1006
Reminded users to run synapse login --rememberMe after schematic init step in ReadMe by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1004
Added the option to populate manifest as an excel spreadsheet to avoid sending metadata to Google APIs by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/994
For schematic APIs, return excel file instead of excel file path by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/988
Emphasized that users should download the config.yml from develop branch in ReadMe by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1007
Removed validity requirement for unrequired attribute entries, allow users to specify validation rule conformity required for entries, fix DCA disconnect caused by JSON Schema validation errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1000
Strip hyphens from Synapse annotation keys by @milen-sage in https://github.com/Sage-Bionetworks/schematic/pull/1020
Fixed a bug where in some instances manifests would be uploaded with different display and downloadAs names by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1017
Added an API endpoint to check if a given node is required or not by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1024
added more instructions of running CLI in jupyter notebook by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1031
Added a slack bot to notify successful new releases by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1025
Turned service_account_creds.json as an environment variable and default way of authentication by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1015
Changed base docker image and removed package for security reasons by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1037
Add support for treating date entries as type datetime by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1041
Automatically updated CLI documentation on Readthedocs by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1047
Deprecated token pickle and credentials.json by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1040
Introduce tests to cover current table operations: creation and replacement by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1046
Skip api tests when rule combination tests are run by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1068
Added workflow to deploy schematic docker container in Github container registry by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1062
Remove schematic support for Python v3.7 and v3.8 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1090
Refactor table operations structure in asset store by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1069
Added input_token as a parameter for /manifest/get endpoint to fix credential issues when getting an existing manifest on AWS by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1080
Fixed getProjectManifests function in synapse storage by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1084
Develop api node display names by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1094
Create API endpoint for get_node_validation_rules by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1095
Update schematic dependencies by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1092
Raise errors for wrong schema errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1073
Set default of "table_manipulation" as "replace" in API endpoint when users enter None and updated tests by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1115
Update synapseClient dependency and api for manifest table uploads by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1101
set pyopenssl = "^23.0.0" by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1125
added date GE rule by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1103
Implement table upsert feature by using schematic-db by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1081
Add use_schema_label parameter to manifest submission endpoint, separate manifest submission and table upsert tests by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1129
Delete GE checkpoint after completion of GE validation by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1136
Remove try: catch: block from manifest submission command function by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1130
Save all properties that are Included in the domain of a Class by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1134
Display exceptions raised during validation with Great expectations, allow exclusion of upper bound OR lower bound for inRange rule by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1131
Update Documentation - python/package versions and POCs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1139
Increase buffer size to a higher limit to deal with long token by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1144
lock schematic-db to version 0.0.6 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1145
use try: finally: to delete checkpoint even if running the checkpoint fails or errors out by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1155
Allowed CORS on given routes instead of all routes by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1168
Added restrict rules param to manifest/validate by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1178
Bug Fix: remedy negation of table manipulation specification by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1186
Added an endpoint to check entity type on Synapse and an endpoint to check if an entity is in the asset view by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1078
add restrict rules control to manifest validate by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1189
Added a parameter to control if GE gets used when using manifest/validate endpoint by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1177
Propagate logger level entered in from command line to other schematic submodules by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1180
Add timing of validation operations to DEBUG log by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1181
Standardize validation error format and type by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1183
Added function to calculate and clear cache by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1190
Develop add file only manifest submission option by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1175
Create example data model for single rule benchmarking by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1193
Develop api tests for benchmarking single rule validation performance by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1184
Fixed column headers problem when generating an Excel spreadsheet for getting an existing manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1164
Do not index attribute visualization dataframe when converting to csv for component viz endpoint by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1196
Remove restrictions on rule number and allowed combinations by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1203
Start checking mypy and black by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1204
Add IsNA rule to validation suite | FDS-81 FDS-232 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1200
Add API endpoint to visualize attributes for a specific component by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1195
Added functionality to download a manifest by using the manifest id by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1192
Introduce workflow for API tests by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1208
Remove requirement for .synapseConfig file to use upsert feature by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1207
Parallelize operations in load_df by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1100
Id Column - fix bug preventing table updates by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1214
Id Column - fix bug where there would be two columns with uuid values by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1215
Merge AWS deployment branch to develop by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1142
Id Column - fix bug preventing upserts by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1216
Downloaded manifests to temporary folders on AWS by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1210
FDS-293 Fix column mismatch for Excel File Based Manifest Generation by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1213
Feature fds 361 pylint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1212
Changed workflow to run poetry version 1.2.0 by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1222
remove breakpoint from command by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1224
Restrict typing-extensions package to versions before v4.6.0 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1228
Make aws group dependencies optional and restrict typing_extensions package version by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1227
Change Uuid column name to Id by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1211
Avoided publishing minor releases to Docker Hub by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1231
Remove lock on schematic_db version - FDS-287 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1232
feat: added nginx to encrypt the communication between ALB and API by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1202
Installed schematic in docker file by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1230
fix: Fixed unit test in test_manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1233
Fix formatting issues when pulling data from Synapse to Excel Manifest by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1234
fix: fixed tests in test_api.py by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1225
Added test manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1238
[Bug fix]: Tried install pdoc again in github action workflow pdoc.yml by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1239
Replaced synapse API calls with synapse Python client call by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1235
Feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1241
Added hide-blanks parameter when submitting manifest through API by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1242
Revert "Feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment" by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1243
feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1244
[Bug fix]: Fix regex in docker build workflow by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1246
Revert "[Bug fix]: Fix regex in docker build workflow" by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1248
[Bug fix]: Fix regex in docker build workflow by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1249
Feature fds 273 coniguration by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1219
Expose strict_validation option for manifest/generate endpoint by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1253
Optimize performance in table upsert backwards compatibility scenarios by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1229
Fix df_utils/load_df so it more accurately captures integers to prevent Regex Errors. by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1240
Use FAIR Data service desk for issues by @afwillia in https://github.com/Sage-Bionetworks/schematic/pull/1257
Update Black to 2023 version: 23.7.0 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1262
Update mypy to latest version by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1263
Updated cli help text for parameter json_schema by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1264
Modified Nginx parameters to fix submission issue by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1255
modify tag by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1251
BugFix: Fixed an issue where files on synapse were not being annotated correctly by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1254
[bug fix] Fixed errors when calling get_empty_manifest by @linglp in https://github.com/Sage-Bionetwork
Sage-Bionetworks/schematic: v23.9.3
What's Changed
BugFix: is_class_in_schema no longer errors out when a class is not in schema by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1287
BugFix: Fix error when use_annotations=True for record based metadata where there are no existing annotations by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1285
Bug Fix: Adding annotations to files with -mrt file_only parameter by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1290
Develop markers for api tests according to credentials required FDS-1026 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1289
Full Changelog: https://github.com/Sage-Bionetworks/schematic/compare/v23.9.2...v23.9.
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community
Recommended from our members
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community