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Beacon Extensions

Chair: Jordi Rambla

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Agenda

Topic

Presented by

Time

​

General introduction

Jordi Rambla

5’

1.1

OMOP

Sergi Aguiló-Castillo

15’

2.0

RNAGet

Emilio Palumbo

15’

2.1

EJP-RD

Tony Brookes

15’

3.0

Cancer registries

Jordi Rambla

15’

3.1

Beacon 4 images

Jordi Rambla

15’

4.0

Wrap-up

Jordi Rambla

10’

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Beacon-OMOP CDM

Sergi Aguiló-Castillo

This work has been funded by the Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”).

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OMOP CDM

Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)

  • Merge disperse databases into a common format (data model).
  • Common representation (terminologies, vocabularies, coding schemes).
  • Widely used to share secondary use of research data in hospitals around the world.

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Beacon RI API

https://github.com/EGA-archive/beacon2-ri-api

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Beacon RI API

https://github.com/EGA-archive/beacon2-ri-api

OMOP CDM

Relational database

We have hijacked the API to query the new database

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Beacon RI & OMOP CDM

https://gitlab.bsc.es/impact-data/impd-beacon_omopcdm

  • Implementation based on the RI-API
  • Query relational DB instead of a NoSQL
  • Individuals, Biosamples and Cohorts models from Beacon
  • Mapping between OMOP CDM and Beacon made by experts
  • No need of convert anything, SQL queries on-the-fly directly to database

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Beacon RI & OMOP CDM

https://beacon.omop.bsc.es/api/individuals?filters=SNOMED:62106007

"Concussion with no loss of consciousness"

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Next steps

  • More testing, with real data, for corner cases.
  • Beacon RI All-in-one: User can choose the type of database (MongoDB or OMOP CDM, for now).
  • More schemas: Genomic or Radiology extension of OMOP CDM? (talk on that later in the session)
  • Suggestions?

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RNAget

Emilio Palumbo

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Introduction

RNAget: an API to securely retrieve RNA quantifications

Bioinformatics, Volume 39, Issue 4, April 2023, btad126, https://doi.org/10.1093/bioinformatics/btad126

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Motivation

  • lack of discovery, searching and filtering capabilities, e.g.:
    • filter expression matrix by expression values
    • look for datasets with a specific expression for a set of features
    • given a dataset, look for samples with a specific expression for a set of futures and extract metadata

→ use beacon framework

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Motivation

  • adding context (e.g. samples and features metadata)
    • harmonised metadata model

→ use beacon model

​

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Requirements

  • feature model
    • feature object
      • Can be gene, transcript, genomicLocation, etc.
      • Has attributes, e.g.: name, referenceAnnotation, type
    • get feature identifier by feature attributes (to be used in expression queries)
    • SequenceAnnotation group

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Requirements

  • expression-specific filtering
    • define filter payload (extend one of the filteringTerms definitions or add a new one)
    • query multiple features by expression value
    • query by expression range

​

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European Joint Program on Rare Diseases

Prof .Anthony J. Brookes

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biobank

registry

Tools catalogs

Registries/�biobanks catalogs

Cell lines

Animal models

Data deposition

&analysis

platforms

Knowledge bases

Support for clinical/

translational research

Find

Query

Analyse

https://vp.ejprarediseases.org

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GA4GH, IRDiRC, ELIXIR, BBMRI, . . .

  • DUC/CCE: Co-lead - digital structure for consent and use conditions
  • Beacon-2: Co-lead - API for federated querying and data sharing
  • OMOP: Use - common structure for health related data
  • Omics data: Use - file formats for high dimensionality data
  • CDE & DS-CDE: Develop - RD core & domain-specific data elements
  • Metadata: Develop – DCAT extensions for cohorts, data/samplesets, etc
  • Phenopackets: Use - validate and consume (Originator installing CV)
  • Security approaches: Use – ensure security of data and software

Standards Based (international)

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Querying

​

​

= Implemented�

​

https://github.com/ejp-rd-vp/vp-api-specs

/catalogs endpoint

/individuals endpoint

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• Range responses

• MinRange and maxRange employed in “info” within “results”

• With resultCount being the minRange

​

• Usage of “arrays of values” in filters, so that multiple terms can be queried

• ‘OR’ logic between terms

​

• Support partial queries

• Warning “info” within “results” to specify unsupported filters

​

• Introduction of auth-key in a custom header for security purposes

​

• Need improved semantic support in responses [e.g., application/json-LD]

Beacon ‘Enhancements’ required to enable EJP-RD

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Beacon for Cancer Registries

Jordi Rambla

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Beacon for Cancer Registries

Idea born in the EOSC4Cancer project

From screening & registries to clinical trials

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Beacon for Cancer Registries - EOSC4Cancer

Prevention

Cancer origin

Diagnostics

Primary tumours

Treatment

Metastatic Cancers

► Cancer registries

► Environment

(pollutants)

► Social data

► Geolocalisation

Cancer Registries

Research Software for epidemiological level analysis

Software, Workflows and Portals for patient level clinical research

Clinical Decision Support Systems

► Screening

programmes

► Medical imaging

► Medical data

(EHR structured

data)

​

Screening Programmes

​

► Patient level:

Genomics data, Imagin (digital pathology), and EHR data (structured data)

► Other research

data: liquid biopsy, animal models, drug screening

► Non patient specific data: animal models, drug screening, etc

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Cancer Research

► Cancer clinical trials (descriptors - metadata)

► Patient level genomics and medical data

► Actionable data (regulated): markers, drugs, and treatments

Clinical trials

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Beacon for Cancer Registries - ENCR

  • Cancer Registries have data at individual level
  • Cancer Registries publish statistic studies about cancer incidence in a given population… therefore, some aggregated/precomputed information is publicly available
  • Cancer Registries in Europe follow the European Network of Cancer Registries (ENCR) recommendations
  • These recommendations include a data model for sharing data

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Beacon for Cancer Registries - Proof of Concept

  • We used the ENCR Model instead of Beacon v2
  • It is simple, just one table, includes data on:
    • Individual
    • Disease onset
    • Disease recurrent
    • Treatment
    • …
  • Attributes highly codified

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Beacon for Cancer Registries

DEMO

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Beacon for Cancer Registries - Next steps

  • Discussed with intramural partners
  • Present and gather feedback from
    • Unveiled today - GA4GH Connect
    • EOSC4Cancer General Assembly - Next week
    • ENCR Annual meeting - Granada Oct’23
  • Analyze the feedback and draft a plan

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Beacon for Images

Jordi Rambla

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Beacon for Images (B4I)

  • Idea born in the IMPaCT-Data and EUCAIM projects
  • Imaging is a huge domain, B4I focuses on radiology

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Beacon for Images (B4I) - Proof of Concept

  • We extended the Beacon v2 Model
  • Follows the OHDSI OMOP approach, looking at the radiology extension
  • Includes data on:
    • Individuals
    • Image acquisition and processing
    • Image features
    • …
  • Attributes highly codified in OMOP Dictionaries

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Beacon for Images (B4I)

DEMO

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Beacon for Images (B4I)

  • Discussed with intramural partners
  • Present and gather feedback from
    • Unveiled today - GA4GH Connect
    • IMPaCT-Data General Assembly
    • EUCAIM
  • Analyze the feedback and draft a plan
  • Integrate the PoC into the OMOP Beacon

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Wrap up!

Jordi Rambla

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