Self-service

STARR Tools

Launched in 2008, and formerly known as STRIDE, STARR Tools currently support a Cohort tool and a Chart review tool. These are intuitive web based interactive tools based on Stanford in-house data model. These tools are easy to use, seamlessly integrated with research compliance processes and offer ease of use. A Data Privacy Attestation is required for Chart Review. STARR Tools platform has been running on Google Cloud since 2021. Access to these tools requires a fully sponsored SUNetID.

OHDSI ATLAS Cohort Analysis Tool

Launched in Q1 2020, this web based interactive cohort tool from OHDSI community runs on top of a non-human subject dataset, specifically OMOP-deid-lite. ATLAS is an open-source software tool for researchers to conduct scientific analyses on standardized observational data. The data is refreshed weekly. This tool is particularly suitable for researchers who want to use community defined study protocols in a GUI environment. Stanford ATLAS has the execution engine turned on, thus making is easier to run network studies.

You need a full sunetid to access ATLAS and the underlying OMOP-deid-lite database. Log in the Stanford ATLAS with your SUNetID using the DUO authentication. Note: You will probably not be able to actually explore any cohorts - you will probably see an error. This step is necessary for the system to create a user id for you. To gain access to OMOP-deid-lite dataset in ATLAS, sign Data Privacy Attestation (DPA) {click the new tab and in the “Project Type”, please select “STARR Nav deID data”}. Do this step only if you haven’t signed STARR Nav DPA before. Note that “Nav” stands for Navigator and signifies a collection of pre-IRB (sometimes referred to as non-human subject) clinical datasets. If you already have access to OMOP-deid data on BigQuery via Nero, you have already completed your DPA requirements. Once you have logged in, please email starr-omop-support@stanford.edu with “Requesting ATLAS access - STARR OMOP ” in the subject line along with your SUNetID. You will receive an email with more information once you have been granted access.

If you are only running network studies or population health studies, access to ATLAS may be all you need. If you need human subject data, you can take a list of de-identified patient IDs developed using ATLAS and after you receive IRB approval, you can request a list of MRNs and related patient data via a data service consultation request. 

Advanced Cohort Engine (ACE)

Launched in Q2 2022, the Advanced Cohort Engine (ACE) is a web tool that combines a unique temporal query language to search and extract patient data. It is particularly suitable for time-aware search of longitudinal patient records with a patient object datastore for rapid electronic phenotyping, cohort extraction, and exploratory data analyses. ACE operates over data in the Observational Medicine Outcomes Partnership Common Data Model, and is configurable to balance performance with compute cost. ACE’s temporal query language supports complex time-based searches and automatic query expansion using clinical knowledge graphs. 

ACE was developed at Stanford in Dr Nigam Shah’s lab. More details are available in the publication. The R and Python APIs are available in a public GitHub repository.

The Stanford Medicine’s instance of ACE, which operates over the latest extract of de-identified STARR OMOP is available at https://ace-prod.med.stanford.edu. You will need to be connected to the Stanford VPN, and have a full sunetid to access ACE. Please Sign the Data Privacy Attestation (DPA) {click the link, and "new" tab and in the “Project Type”, please select “STARR Nav deID data”}. Email starr-omop-support@stanford.edu, “Requesting ACE access” in the subject line. 

Learn more about how to use ACE  (accessible with sunetid)

Pre-IRB OMOP database

Launched in Q4 2019, the OMOP-deid database is a pre-IRB direct SQL access to de-identified High Risk dataset, in OMOP Common Data Model. The dataset is a non-human subject dataset and contains complete clinical text as well as clinical concepts derived from text processing. Additionally, OMOP supports complex electronic phenotyping. Hosted on Google Cloud Platform BigQuery analytical data warehouse, researchers can access from their secure Nero workspace. 

You need a full sunetid to access OMOP-deid database. Sign a Data Privacy Attestation (DPA)  {click the link, and "new" tab and in the “Project Type”, please select “STARR Nav deID data”}. Note that “Nav” stands for Navigator and signifies a collection of pre-IRB clinical datasets. Request a Nero account - a Stanford PI affiliation is required for a Nero account. In some exceptional cases, Stanford Directors and C-suite executives can act as PI. Specify that you are requesting access for STARR-OMOP-deid. You will need a Nero GCP account. Once a Nero project has been created, you will get an email from Stanford Research Computing Center (SRCC) informing you that access has been granted with some introductory information.  Email starr-omop-support@stanford.edu with “Requesting STARR-OMOP-deid data in BigQuery” in the subject line and your Nero GCP project name and your PIs ORCID.

If you are doing population health research or a network study, chances are, you never need identified data and you can simply use the OMOP-deid or OMOP-deid-lite, the later dataset has no TEXT or TEXT_NLP. A limited data set or human subject data in OMOP CDM is accessible via data services consultation request.

Pediatric bedside monitoring data

Launched in Q1 2021, the wave-deid metadata database is a pre-IRB direct SQL access to de-identified High Risk dataset. The dataset also contains de-identified and linked waveform data in PhysioNet format. Hosted on Google Cloud Platform BigQuery analytical data warehouse and Google Cloud storage, researchers can access from their secure Nero workspace. 

To access this non human subject dataset, first sign a Data Privacy Attestation (DPA) - click the link, and "new" tab and in the “Project Type”, please select “STARR Nav deID data”. Note that “Nav” stands for Navigator and signifies a collection of pre-IRB clinical datasets. You will need a Nero GCP account. Once a Nero project has been created, you will get an email from Stanford Research Computing Center (SRCC) informing you that access has been granted with some introductory information. Email starr-omop-support@stanford.edu with “Requesting STARR wave deid data in BigQuery” in the subject line and your Nero GCP project name and your PIs ORCID. 

The post-IRB identified version or limited dataset is accessible via data service consultation request.