A standard nomenclature is incredibly valuable for teams using LabKey Server to do collaborative biomedical research and becomes increasingly more important as they grow in size and data volume. Defining how data fields should be named is essential to the efficiency of teams, as it aids both those generating and/or capturing data as well as those conducting data analysis.

As you get started using LabKey Server, keep in mind the best practices below for defining and maintaining a standard nomenclature in your lab:

Define Nomenclature Up Front

Standardizing nomenclature may seem like an unnecessary up-front investment, but ultimately your team will experience less confusion and more efficiency as they progress with their work. Empower your team by allowing them to have a voice as you define which terms will be used in your research. By including team members in the process, they will feel more invested and be more likely to adhere to standard naming conventions.

Use LabKey QC Features to Ensure Consistency

In an ideal world, all team members will consistently use the nomenclature agreed upon by the team when adding data to your LabKey Server. But in practical application, it is more likely that from time to time a team member will mistakenly enter “H20” instead of the lab standard name “Water” into their ingredient list, potentially breaking standard reports, grid views, etc.

Using LabKey quality control features like lookups, aliases, and validators in key fields can help combat this scenario. A LabKey lookup will allow you to to map several common variations of a term to a desired standard field value. For example, an administrator could configure a lookup so that “H20” and “Tap Water,” common deviations from the standard, would both map to “Water.” These types of lookups allow teams to maintain the integrity of their data, in spite of inevitable human error.

Administrators can also use to regex or range validators on new data being entered to ensure that users are entering valid data into the system. By placing these restrictions, teams can improve data entry and help analyses down the pipeline.

Evaluate and Adjust

It’s easy to enforce the use of standard nomenclature when your team is small and your research is in its early stages. But over time, as teams grow and become further removed from when nomenclature guidelines were established, they can develop a “laboratory shift” in how things are named. In order to stay on top of your terminology and keep your data clean, plan to regularly review and assess your standard nomenclature. Are there additional terms that need to be defined? Have any standard terms become outdated? Are certain terms consistently being used incorrectly? Making small adjustments as your research needs evolve will help maintain the integrity of your data.

LabKey helps enforce nomenclature standards, leading to cleaner data and more efficient research. Sign-up for a free trial to see these and other core LabKey Server features in action. 

Related Documentation

• Lookup Columns 
• Field Level Validation
• Data Quality Control

Integrated NLP data management solution speeds clinical data abstraction and curation for disease registries, clinical research and quality reporting

Cambridge, England and Seattle, WA, USA — September 25, 2018 — Linguamatics, the leading natural language processing (NLP) text analytics provider, and LabKey, a provider of bioinformatics data management solutions, today announced an integrated solution designed to streamline the extraction and curation of valuable insights from large volumes of unstructured clinical notes and reports.

With Linguamatics NLP engine I2E, healthcare and life sciences teams can significantly reduce the manual processes involved in information analysis and extraction. When integrated with LabKey Server’s document processing pipeline and curation user interface (UI), the combined solution provides an end-to-end pathway for unstructured data from acquisition to analysis.

“Our partnership with LabKey empowers healthcare teams to achieve high accuracy data extraction in a wide variety of use cases” said Simon Beaulah, senior director, healthcare at Linguamatics. “Customers can speed extraction of EHR data into cancer registries and clinical data warehouses; reduce the manual burden associated with clinical study review; and rapidly extract relevant population health data and quality metrics to improve business critical HEDIS quality metrics reporting and patient outcomes.”

The LabKey and Linguamatics relationship is based on collaborative work with the NCI’s Surveillance, Epidemiology, and End Results (SEER) Program. This project has resulted in an NLP pipeline that automates the annotation and review of pathology reports, to build a large gold standard for machine learning training.

“Combining LabKey’s processing pipeline, workflow, and curation UI with Linguamatics’ NLP capabilities provides a complete solution for organizations that need to extract valuable information from large volumes of unstructured clinical data,” explained Adam Rauch, vice president of product management at LabKey. “This integrated system empowers abstractors and reviewers with the technologies they need to accelerate the extraction process from end-to-end.”

About Linguamatics

Linguamatics transforms unstructured big data into big insights to advance human health and wellbeing. A world leader in deploying innovative natural language processing (NLP)-based text mining for high-value knowledge discovery and decision support, Linguamatics’ solutions are used by top commercial, academic and government organizations, including 18 of the top 20 global pharmaceutical companies, the US Food and Drug Administration (FDA) and leading US healthcare organizations.

Linguamatics I2E is used to mine a wide variety of text resources, such as scientific literature, patents, Electronic Health Records (EHRs), clinical trials data, news feeds, social media and proprietary content. I2E can be deployed as an in-house enterprise system, or as Software-as-a-Service (SaaS) on the cloud.

About LabKey

LabKey provides software solutions to help teams overcome the data management and workflow challenges faced in today’s biomedical research environment. LabKey works hand-in-hand with clients to understand the complex needs of modern labs and develop flexible, scalable, extensible systems to address them.

LabKey Server is an open source software platform for integrating biomedical research data and managing laboratory workflows. LabKey Server is highly configurable and is used by research organizations across the globe to provide reliable, scalable environment for research data. [vc_row gap=”30″][vc_column width=”1/2″][vc_column_text css=”.vc_custom_1537808118148{padding: 30px !important;background-color: #ededed !important;}”]

LabKey Media Contact

Kelsey Gibson, Marketing Manager
LabKey

+ 1 425.308.7033
kelseyg@labkey.com[vc_column width=”1/2″][vc_column_text css=”.vc_custom_1537808128682{padding: 30px !important;background-color: #ededed !important;}”]

Linguamatics Media Contact

Michelle Ronan Noteboom, Sr. Account Director
Amendola Communications

+ 1 512.426.2870
mnoteboom@acmarketingpr.com

CAR T and other cellular immunotherapy trials are rapidly expanding worldwide due to their high success rates and continued scientific advancements that are helping generate new therapeutic targets. The development of these advanced immunotherapies requires extensive data collection and collaboration between research scientists, clinical teams, and trial subjects. In order to manage immunotherapy data efficiently and improve the feedback loop from current and ongoing trials many research teams are seeking out secure, web-based data management solutions in lieu of traditional paper based systems to manage their trial data.

LabKey is actively partnering with teams conducting immunotherapy trials to provide LabKey Server-based solutions to overcome a wide variety of challenges and accelerate their research, including:

Integrating Heterogeneous Immunotherapy Data

Cutting edge cellular immunotherapy trials rely on data generated at multiple sources often including the cellular manufacturing facility, the clinic gathering subject data, and research labs exploring the cellular profile of the therapy. Teams conducting CAR T and other immunotherapy trials need reliable software tools to integrate this heterogeneous data and provide a comprehensive view of the therapy’s efficacy and safety to clinicians and researchers.

LabKey Server helps immunotherapy research teams efficiently integrate heterogeneous data by providing:

• A data-aware study module that can recognize and integrate disparate vendor datasets, alias subjects and track visits by name or by date
• Built-in and customizable integration with electronic data capture systems and case report forms

Longitudinal Study Data Capture

Lengthy follow-up periods are typically required for subjects undergoing therapy involving genetically modified cells. Managing trial data over time in a secure and scalable manner quickly becomes very challenging for paper-based systems.

LabKey Server helps support the consistent collection and storage of longitudinal study data throughout the lifetime of a trial by providing:

• A configurable study progress report that allows trial staff to manage samples and tests, ensuring that every result is accounted for.
• The flexibility to customize and modify the system as the needs of the database grow and change, without compromising historic data.
• Professional support and services to ensure that the system is maintained throughout the life of the trial.

Explore this Longitudinal Study in LabKey Server

This example study compares various anti-retroviral (ARVs) treatment regimens by monitoring HIV-1 disease progression in 122 participants.

Compliant Collaboration

Sharing reports and data with collaborators improves research, innovation, and ultimately subject care. Maintaining compliance and having the ability to quickly share data and reports is an important topic to tackle in immunotherapy research where subject safety and care is the top priority.

LabKey Server improves reporting and collaboration amongst collaborators conducting immunotherapy trials by providing:

• Dynamic and static reporting tables and visualizations that can be shared as-needed
• Web-based access to a central platform for data sharing
• The ability to remove PHI fields or provide randomized IDs when sharing
  information with collaborators

[vc_cta h2=”Explore LabKey Server” add_button=”bottom” btn_title=”Start Your Trial” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_shape=”round” btn_align=”left” btn_link=”url:https%3A%2F%2Fwww.labkey.com%2Ftrial-sign-up%2F|||”]With the right tools, immunotherapy research teams can push the pace of this cutting edge research even further, increasing trial efficiency to bring life saving therapies to more patients faster. Sign-up for a free trial to see how LabKey Server can help your team overcome these, and other common immunotherapy research challenges.[/vc_cta][vc_custom_heading text=”Related Resource” font_container=”tag:h1|text_align:left” google_fonts=”font_family:Roboto%3A100%2C100italic%2C300%2C300italic%2Cregular%2Citalic%2C500%2C500italic%2C700%2C700italic%2C900%2C900italic|font_style:300%20light%20regular%3A300%3Anormal” tm_text_transform=”uppercase” css=”.vc_custom_1541533930179{padding-top: 10px !important;padding-bottom: 10px !important;}”]

User Presentation

Using Existing LabKey Modules to Build a Platform for Immunotherapy Clinical Trials

The Correlative Studies Laboratory (CSL), part of the Immunotherapy Integration Hub at Seattle Children’s, focuses on understanding how reprogrammed T cells react in each patient in terms of their persistence, functionality and efficiency at reducing tumor burden. This data, combined with manufacturing and clinical data generated during clinical trials, enable researchers to answer pressing questions with minimal time and resource investment.

In this presentation Olivia Finney, shares how the CSL is working with LabKey to integrate, analyze and securely share data in order to create a truly translational research model. Watch presentation >

LabKey Server gives teams the flexibility to assign permissions to individual users or to security groups. While teams are setting up and implementing LabKey Server, assigning user permissions individually often seems like the easiest route, but for growing teams or active labs that strategy can become an administrative challenge in the long run. As your team and/or use of LabKey Server grows, it becomes much easier for administrators to control permissions with User Groups.

What’s more important than which method you choose, is taking the time to define your permissions strategy up front. A defined and documented policy will help make managing security easier to implement and maintain long term. Take a look at the best practices below to set yourself up for success when creating a permissions strategy:

1. Define User Groups

Think about the functional requirements of your team; are there members that will need read-only access and some members that need to enter in data? By splitting out what the needs of each person are, you can easily define user groups based on common access needs.

2. Consider Folder Structure

Take your LabKey Server folder structure into consideration when defining security groups; should your team members have the same permissions to all folders? Do certain team members need the same level of access but to different folders? Use your folder structure to help further segment users into appropriate security groups.

3. Monitor and Adjust

Review and refine user groups over time as the use of LabKey Server continues to grow. Administrators should review their permission settings at a regular frequency to make sure permissions for a User Group are accurate and appropriate for the current situation. Use LabKey Server’s Impersonate feature to view access as each User Group and verify that the permissions assigned to each group are correct.

Get started securely sharing data with team members and collaborators using LabKey Server! Sign-up for a free trial to see LabKey Server permission management features in action. 

With ever-increasing technological advancements, basic research laboratories are making scientific discoveries at unprecedented rates. With increasing knowledge and understanding about our world, basic research scientists need affordable ways to improve data management and sharing methodologies. When scientists can perform experiments more accurately and with better reproducibility, they are able to improve data integrity and ultimately quicken time to publication.

In order to be effective in today’s data-rich research environment, scientists are looking to software tools to help facilitate research and time to publication. LabKey Server provides essential tools to overcome key basic research challenges, including:

Effectively Managing Heterogeneous Lab Data

Effective management and merging experimental data can help identify gaps in research or highlight key insights to new discoveries, but manually comparing performance of a particular molecule, cell line, or other entity across experiments a time-consuming and difficult process.

LabKey Server helps teams manage lab data by providing:

• Assay integration modules that directly import and transform lab data, such as luminex, flow cytometry, mass spectrometry, ELISA/ELISpot, and more.
• A flexible, customizable platform that can handle data from team specific assays
• Easy-to-perform data integration

Establishing Good QC Metrics

Creating good quality control methods as part of standard workflows ensure data integrity and ultimately allow scientists to compare data across experiments to collect reliable, reproducible data.

LabKey Server helps enforce good quality control practices by providing:

• Automatic type checks, missing value indicators, and range validators on data
• Built-in QC trend reports, Levy-Jennings and other QC graphs
• Dataset QC states that flag data for review

Collaborative Data Sharing

Sharing data with internal and external collaborators improves scientific integrity and innovation. Effective collaboration reduces duplicative effort, quickens analytical time, and improves data integrity, enabling cross-functional work and quicker development of discoveries.

LabKey Server facilitates collaboration by providing:

• Multi-level security permissions, giving teams full control of what information they share and who it is shared with
• An assay request tracker that allows teams to collaboratively assign new experiments and track their fulfillment
• Study publishing tools that de-identify data, allowing collaborators to examine data and analyses without interfering with the raw data

Want to see how LabKey Server can help increase data workflows in your basic research environment? Explore these, and other features, of the LabKey Server platform with a 30-day hosted trial. Get started >

Modern research technologies have greatly increased the amount of scientific data being generated, but making full use of that data is still a major challenge. Data accessibility is a consideration at all stages of the research process; for bench scientists making data accessible to informaticians, for teams sharing data cross-departmentally, and for researchers making data accessible to the public.

The accessibility of data is essential for a number of reasons:

1. Minimizing Data Redundancy of Research Efforts

Research redundancy is a major problem within research organizations and across the research community. By making data accessible to their desired audience, researchers can reduce the number of redundant experiments conducted and instead iterate upon existing research to accelerate discovery.

2. Drawing More Reliable Conclusions from More Data

Broader data accessibility allows research teams to pool data and conduct analysis with greater confidence in their results. The more data a researcher has access to, the more statistical power they have to validate research conclusions and preempt questions of data quality.

3. Inspiring Novel Questions from Different Approaches

New research questions are inspired by different research approaches and through the study of new methodology. Attacking scientific investigations from varying perspectives also helps reduce bias in analytics, experimental design, and conclusion drawing.

Expanding Data Accessibility with LabKey Server

LabKey Server not only helps teams collect and curate their data, but also helps make it accessible to collaborators and downstream researchers.

Web-Based Access

LabKey Server allows researchers to make their data accessible to a broad or narrow audience through a web-based portal. Web-based access makes it easy to share data as desired and allows interested collaborators to evaluate and alternatively analyze “self-serve” research data. This method of data sharing is both more secure than email (see fine grained permissions below) and much lower overhead than a standard institutional database as users can query, view, and export data without having to interface with a data scientist.

Fine-Grained Permissions

LabKey’s fine-grained permissions model makes secure, selective sharing of to data simple and reliable. With LabKey Server, teams can easily control who sees their data, restricting access to selected individuals or pre-defined groups, or making data accessible the general public. Researchers also have fine-grained control over what datasets are shared: either a single table of data or an entire research project.

Powerful Metadata

LabKey Server captures detailed metadata to help increase discoverability of research data and provide crucial context for other researchers who hope to explore, reanalyze, and/or expand upon it. Research teams can customize metadata captured for each of their data types and add organization specific metadata to support internal needs.

Interested in learning more about how LabKey Server can enhance the accessibility of your research data? Contact the LabKey team for more information or request a demo!

*To learn how configure accessibility features of LabKey Server, read documentation >

High-throughput analysis techniques are incredibly powerful and provide teams with more data than ever. While that depth of data often holds the key to scientific insights, organizing such large quantities of data in a consistent and discoverable way has become a major challenge for research teams.

Many teams rely on spreadsheet-based systems to organize and manage their data. This approach becomes less-effective as research scales because spreadsheet-based strategies lack two essential characteristics:

1. Consistency

Manual file management relies on the individual contributor’s abilities to consistently create, name, and store data files. This opens the door to a wide range of human errors that will ultimately impact the discoverability and reliability of your data. Common consistency errors that result from manual data management include:

• Poorly named files
• Inconsistent locations
• Duplicate files

2. Discoverability

Collecting data is a giant hurdle in research, but in reality, it is just the first of many. Researchers need to be able to locate datasets of interest in order to conduct analysis. In a file based environment, discoverability of files is dependent on the consistency with which they are maintained. Were they saved in the correct location? Have they been named according to an agreed upon convention? Is there a clear authoritative file or are there duplicates?

A hitch in any one of these areas can severely hinder the discoverability of your data and make it significantly more difficult to:

• Track what research data has already been collected
• Find the data you are looking for when it comes time to analyze

Biology-Aware Data Management with LabKey Server

Scientific data management systems like LabKey Server, help increase the consistency and discoverability of your research data. LabKey Server increases the consistency of data management by providing structured data grids for storing various type of research data. Each data grid type also captures relevant metadata, specific to that data type, in order to help make data more discoverable.

Research-Centric Data Structures

Unlike spreadsheets that treat all types of data the same, LabKey Server provides four primary data structures with unique features to better support common types of research data.*

LabKey Assays – Assay data grids capture data generated from individual experiment runs. Assay data is automatically structured in a batch-run-results hierarchy when data files are added. LabKey Server supports data a variety of common assay designs out of the box, but teams can also design their own assay data structure using LabKey’s General Purpose Assay Design.

LabKey Datasets – Datasets track patient/subject measurements over time. LabKey datasets are automatically aligned and joined together, making it easy to query the integrated data and to create visualizations from multiple datasets.

LabKey Specimens – Specimen repositories track the status of each specimen and vial in your inventory. Built-in reports provide a birds-eye view of specimen information, and advanced search capabilities allow for easy location of specimens.

LabKey Lists – LabKey lists provide general purpose, online, interactive grids for any tabular data. Data stored as a LabKey list can be sorted, filtered, and visualized using built-in tools.

Storing data in a consistent, structured manner is the key for teams that hope to achieve maximum efficiency in operations and maximum value from their data. Not only is it much simpler to find data when it is stored in an expected location, but the centralization and integration makes it possible to query data to more quickly locate information of interest.

Interested in learning more about how LabKey Server can increase consistency and discoverability of your research? Contact the LabKey team for more information or request a demo!

*To learn how to add data to LabKey Server, read documentation >