MD/MSPA Students

Key Databases

General Research Resources

Data Resources at Stanford Medicine

Lane Library's Bioinformatics Office Hours is only one of the myriad of services at your disposal as a member of the Stanford Medicine community. The list below includes services that are available to help you address questions related to data collection, analysis, and storage. For additional help with any of Stanford's cluster services (Sherlock, Nero, Farmshare, etc), contact SRCC support.

Please note that, while Bioinformatics Office Hours is a free service, some of the services below operate on a cost-recovery model or through special arrangements with specific departments or units.

Statistics Consulting by the Department of Statistics

The Department of Statistics offers a free online consulting service to members of the broader research community during each Stanford academic quarter. Under the supervision of a senior faculty member, Statistics graduate students arrange meetings with clients to help with statistical research questions in areas such as:

  • Experimental design and data acquisition
  • Data exploration, analysis, and interpretation
  • Modeling data and model fitting
  • Statistical inference for estimation, testing, and prediction
Social Science Data and Software

Social Science Data and Software (SSDS) is a group within the Stanford Libraries that provides services and support to Stanford faculty, staff, and students in the acquisition, curation, and preservation of social science data and the selection and use of quantitative (statistical) and qualitative analysis software. SSDS staff members provide these services in a variety of ways that include consulting, workshops, and help documentation. 

Quantitative Science Unit

The Quantitative Sciences Unit (QSU) is a unit of statistical scientists in the Department of Medicine who engage in interdisciplinary research.  Members of the QSU are available to collaborate on study design and analysis for medical studies.  The QSU offers professional data analysis using the most modern statistical techniques and secure HIPAA- and IRB-compliant management and coordination of data. 

The QSU facilitates medical research for faculty on the medical campus in the following areas:

  • Study design
  • Data analysis
  • Methods and software development
  • Data management and coordination
  • Education and training
Data Studio

The Data Studio is a collaboration between Spectrum (The Stanford Center for Clinical and Translational Research and Education) and the Department of Biomedical Data Science. The Data Studio is open to the Stanford community, and we expect it to have educational value for students and postdocs interested in biomedical data science. Most sessions are an extensive and in-depth consultation for a Medical School researcher based on research questions, data, statistical models, and other material prepared by the researcher with the aid of a facilitator. The last session of each month is devoted to drop-in consulting. BDS faculty are available to provide assistance with your research questions. Bring any data, prior analyses, or other materials that you have. No advance notification is required. 

Research IT

Research IT has built and operated STRIDE since 2008 and Stanford REDCap since 2010. These resources are paid for by Dean's Office and support 1000s of researchers at Stanford. Their platforms meet Stanford regulatory requirements, are petascale, cloud-enabled, and use a variety of sophisticated technologies. Research IT also uses their expertise to support smaller projects via our consultation services. They have expertise in a number of areas including:

  • Data management strategies: Retrospective, prospective, real-time studies
  • Databases: Oracle, MySQL, PostgreSQL, Google Cloud Platform BigQuery
  • Software development: Multi-tier software, APIs, UI/UX, Java/PHP
  • Common Data Models: i2b2, OHDSI OMOP, PEDSNet
  • Data types and sources: EHR, imaging, omics, environmental, population health, IoT, patient- and device-reported
  • Data collection and storage: Electronic data capture, survey platforms, mobile apps
  • Analytical environments: Servers, High Performance Computing, Cloud
  • Regulatory: HIPAA, 21CFR11, FISMA, NIH dbGaP
  • Security and Privacy: De-identification, Stanford Minimum Security standards
  • Stanford processes: Data Risk Assessments, Human Subject Research, IRB
  • Institutional, multi-party requirements: Data Use Agreements, Business Associate Agreements, Master Service Agreements
  • Hospital ecosystem: Clarity, HL7, SMART on FHIR

Reference Management Software

Reference management tools help you collect, manage, cite, and share bibliographic references. These tools can be used to automatically generate both in-text citations and bibliographies, organize PDFs, and share references between team members. Lane Library recommends Zotero, which can be downloaded and used free of charge, for most users.

 

Reference Management Software helps you:

  • Save time
  • Stay organized
  • Easily save references from databases and the web
  • Create citations automatically
  • Quickly change citation styles

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Zotero is a free reference manager produced by the Center for History and New Media at George Mason University. Notable features include web browser integration, online syncing, generation of in-text citations, footnotes, and bibliographies, as well as integration with the word processors like  Microsoft Word and Google Docs.

Lane Library recommends using the Zotero desktop client alongside the Zotero connector, a bookmarklet that will allow you to save materials from the web to Zotero in a single click as well as Zotfile, a free plugin that automatically renames and manages PDFs and other attachments.

EndNote is a reference manager produced by Clarivate Analytics. If you routinely work on large evidence synthesis projects and use certain features within Covidence, Endnote may be preferable to other reference management options.

A limited version of Endnote is available as part of Lane Library's subscription to Web of Science, but the standalone version must be purchased through the Stanford Bookstore.

Distinguish Yourself with ORCID

ORCID is an alphanumeric code, kind of like a social security number, that identifies you as a contributor to scholarly work.  Lane Library and the other libraries at Stanford recommend that every Stanford-affiliated researcher claim their ORCID.

Why claim your ORCID iD?
  1. Your ORCID iD is unique to you. Not only will ORCID help distinguish you from researchers with the same or similar names, but your ORCID iD will remain the same, even if your name or affiliation changes, maintaining the connection to the work you've done.
  2. ORCID helps you demonstrate all of your contributions. Using ORCID, you can demonstrate your contributions to a wide range of scholarly works, from journal articles and book chapters to posters and presentations.
  3. ORCID helps you connect and integrate. Once you have claimed your ORCID, you can use it to log into and connect a wide variety of profile systems and other tools. For example, Dryad uses ORCID for login and both the uploader and any co-authors can add their ORCID to published datasets.
  4. It is required. A growing body of scholarly publishers and funding agencies have begun to require that researchers list their ORCID iD as part of when submitting a new proposal or work.

Contact your liaison librarian if you have any questions about setting up or using your ORCID iD. For more information about maintaining your researcher identity, see our Research Impact guide. 

There are a variety of ways to claim your ORCID iD and link it to your Stanford credentials. Below we've listed what we think are the most straightforward steps. If you have questions or would like to set up a consultation, please contact your liaison librarian.

Claim your ORCID iD

  1. Register for an ORCID iD on ORCID's registration page. We recommend setting your default visibility setting to "Everyone" so ORCID can help you connect to other profile systems and tools.
  2. Connect your ORCID to your Stanford credentials and authorize Stanford as a trusted organization within ORCID by visiting this authorization page and completing the necessary steps.

Add information to ORCID

  1. Add information about yourself, such as your education and place of employment.
  2. Works, such as journal articles, can be added manually or one at a time using identifiers such DOIs or PMIDs. However, we recommend adding them from another system, such as CrossRef Metadata Search, DataCite, and Europe PMC. 
  3. Remember, you can add posters, presentations, datasets, and other types of work to your ORCID profile. Show off your contributions!

How to import works into your ORCID record using a Search & Link wizard from ORCID on Vimeo.

Why maintain an ORCID profile when you're already maintaining similar profiles elsewhere? Because you can actually use ORCID to connect to many of these systems and share content between them!

One such system is SciENcv (Science Experts Network Curriculum Vitae), the profile system for anyone who applies for, receives, or is associated with research investments from federal agencies like NIH and NSF. Researchers can use SciENcv to create and maintain biosketches that are submitted with grant applications and annual reports.

Link your ORCID and SciENcv

  1. Log into your MyNCBI account. If you do not already have an account, you can log in using your Stanford credentials by clicking on "See more third party sign-in options" and selecting Stanford.
  2. When you see your dashboard, click on "Manage SciENcv" in the "SciENcv" box.
  3. Click "edit" in the grey box. Then complete the required information. Under "optional information", click to add your ORCID. If necessary, log into ORCID to complete the integration.
  4. Congratulations! You will now be able to pull from your ORCID profile to populate SciENcv documents!

For more information, see this video from NCBI or contact your liaison librarian 

In addition to profile systems like SciENcv, ORCID also integrates with a variety of other research-related tools giving you essentially a single sign and enabling you to share information about your contributions throughout your research toolchain. Below we've highlighted some tools that connect with ORCID that are widely used at Stanford Medicine.

Dryad, the open data repository, requires ORCID iDs for login. Once you've logged in and published a dataset through Dryad, you can be added to your ORCID profile as a work. Dryad also allows you to add ORCID iDs for co-authors.
Overleaf, the collaborative LaTeX editor allows you to login with your ORCID iD and connect your ORCID to your current account. Once your account is linked, your ORCID iD will be included when you submit work to participating publishers. 
Protocols.io is a repository for recording and sharing up-to-date research methods and protocols. Connecting your ORCID iD with your account allows protocols.io to post information about your published protocols onto the "Works" section of your ORCID record. 
  • Last Updated: Apr 15, 2024 1:22 PM
  • URL: https://laneguides.stanford.edu/MD-PA-Students
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