Category: Products & Services

17 Oct 2018
Using look ups to standardize laboratory nomenclature and clean data entry

Setting Yourself Up for Success: 3 Best Practices for Using Standard Nomenclature

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 standard nomenclature for scientific research up front.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 lookups in LabKey helps standardize the nomenclature used in your research data.

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.

Regularly evaluate and refine the standard nomenclature you use in your scientific research.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

25 Sep 2018
LabKey and Linguamtics partner to speed Natural Language Processing of Clinical and Unstructured Documents

LabKey and Linguamatics Partner to Extract Clinical Insights from Big Data in Healthcare

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 Natural Language Processing NLP Solutions for Healthcare and Life Sciences

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. 

LabKey Media Contact

Kelsey Gibson, Marketing Manager
LabKey

+ 1 425.308.7033
kelseyg@labkey.com

Linguamatics Media Contact

Michelle Ronan Noteboom, Sr. Account Director
Amendola Communications

+ 1 512.426.2870
mnoteboom@acmarketingpr.com

24 Sep 2018
LabKey Biologics Cell Culture Media Development Software Tools

Data-Driven Tools for Optimizing Cell Culture Media

Cell culture is a central component of protein development and the media used during this process can have a significant impact on its performance. In the R&D environment, media technicians are responsible for both the precise production of cell culture media and the optimization of media recipes to maximize qualities such as growth and stability.

Capturing the detailed information about recipes, ingredients, and batches needed to optimize media production is one of the key challenges faced within protein engineering. The advances in cell culture technologies in recent years have quickly outpaced simple spreadsheet and database-based systems for storing media recipes and batch IDs. Today’s media technicians need software tools to consistently structure data about media recipes, ingredients and batches, so it can be easily accessed and queried on demand.

LabKey Biologics provides essential tools to help protein engineering teams overcome key challenges in cell culture media development, including:

Capture the steps, ingredients, concentrations, and other details of cell culture media recipes in the LabKey Biologics software

Detailed Recipe Registration

Registering a recipe in LabKey Biologics allows technicians to specify all of the information needed for its execution including ingredients, ingredient concentrations, steps for creating the mixture, expiration time, and other key aspects. The system also allows the creation of mixtures that contain other mixtures, even when you don’t know all of their underlying concentrations or ingredients (as is often the case with vendor-supplied mixtures).

Media technicians have a number of different methods available for registering media recipes, depending on their complexity and scale. Technicians can create recipes individually using the media registration UI or they can register many recipes at once using bulk upload features or programmatic registration via LabKey Biologics API.

Software tools for creating consistent cell culture media batches.Consistent Batch Preparation

LabKey Biologics helps minimize formulation errors by auto-calculating the amounts for each ingredient in a recipe based on a target mixture amount. As a technician prepares a batch of mixture, they are prompted to input the actual amount of each ingredient used, as well as the raw material ID. If the media technician needs to use multiple bottles of a raw ingredient to fulfill the formulation, the system will allow them to register multiple raw materials for a single ingredients.

Data driven cell culture media optimization using LabKey Biologics softwareFollowing the Media Trail

The structured data captured in LabKey Biologics allows R&D teams to track the complete lineage of each individual sample, and present lineage as a visualization or grid. Sample characteristics, assay results, and relevant media details are tied together allowing media technicians to troubleshoot problematic raw materials, better optimize their batches, and improve upon media recipes to improve protein yield.

With the right tools, cell culture media technicians can consistently produce media batches and iterate media recipes to maximize performance. Request a demo to see this functionality in action and learn more about how LabKey Biologics can help accelerate your biotherapeutic R&D.

14 Sep 2018
LabKey Server software tools for immunology trial data management

Built for Science: Data Management Tools for Immunotherapy

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 this data efficiently and improve the feedback loop from current and ongoing trials many immunotherapy focused 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:

Connect data from heterogeneous data sourcesIntegrating Heterogeneous 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 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.

Compliant Collaboration

LabKey software tools for sharing scientific data onlineSharing 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

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.

29 Aug 2018
Using security groups to manage access to scientific research data in LabKey Server

Setting Yourself Up for Success: 3 Best Practices for Managing Permissions

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:

Using security groups to manage access to scientific research data in LabKey Server1. 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.

Use a folder structure for organizing scientific research data that supports security in LabKey Server2. 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.

Regularly review LabKey Server security setting3. 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. 

27 Aug 2018
LabKey Biologics registration and classification tools for protein engineers

LabKey Biologics for Protein Engineers

LabKey Biologics registration and classification tools for protein engineersThe focus of pharmaceutical and biotech research has seen a significant shift in recent years. Many research teams are no longer driving towards building small molecules, but are instead focused on designing new protein-based therapeutics.

Protein engineers at these organizations are often responsible for the structural design of target molecules as well as the experimental protein production and characterization of their designs. To support this work, protein engineers need software tools to capture details about molecular components such as proteins, antibodies, plasmids and cell lines, as well as the detailed steps of the development process. LabKey Biologics provides an easy to use system for centralizing this information and additional tools to help facilitate protein design including:

Uniqueness Verification

There are a number of entities that might be critical for a research organization to register. These could include:

  • Protein Sequences
  • Nucleotide Sequences
  • Molecules (ex: Antibodies)
  • Plasmids
  • Cell Lines

Each of these entities is checked for uniqueness when they are registered in LabKey Biologics.  This prevents dirty data caused by duplicate records and reduces duplicate work for protein engineers. Uniqueness checks are in place for all entity types, whether you are registering a single sequence or a molecule composed of multiple protein sequences.

Uniqueness checks are also run on data auto-registered during the import of a GenBank file. In that case, LabKey Biologics will register plasmids during the import of a GenBank file, but also auto-register any regions that translate to protein sequences. If a protein sequence already exists, the system will register only the relationship between the plasmid and that protein sequence, not create a new sequence.

Classification

LabKey Biologics includes a classification engine that can identify, predict, and calculate various characteristics of registered molecules. This saves protein engineers valuable time manually assigning classifications.

The system automatically detects many regions and features of protein sequences including leader sequences, variable regions, constant regions, and CDRs. LabKey Biologics can also be trained to recognize additional sequence classifications, for example, by registering a leader sequences as a “Leader” within the system, it will recognize future leader sequences that match it.

LabKey Biologics can also recognize heavy chains and light chains and predict their type,  based on the amino acid sequence of a registered protein, as well as the isotype of the overall antibody.

For all of these classifications, whether LabKey Biologics is detecting subsequences on the amino acid sequence or the type of overall sequences, the protein engineer can always override the classification engine if the prediction is incorrect.

Integration with Other Systems

Often times, protein engineers are using another application to design proteins or plasmids. LabKey Biologics makes it easy to bring this data into the system, either via APIs or by bulk upload. Regardless of the registration method, the same classification and uniqueness checking features apply to all registered entities.

To see this functionality in action, request a demo! To learn more about LabKey Biologics check out our documentation and resources on the LabKey Support Portal.

09 Aug 2018
LabKey software tools for clinical research data

Clinical Research: Improving Data Management & Reporting

Managing and reporting clinical data has historically included manual curation and compilation of datasets from disparate data warehouses. In today’s data-rich environment, manual processing and integration is becoming more and more of a bottleneck.

In order to keep up with the increasing amount of data collected from clinical research, clinicians and statisticians alike need software tools that will centralize their data and help them quickly recognize errors. LabKey Server provides essential tools to overcome these, and other key clinical research challenges including:

LabKey tools for maintaining data integrity in clinical research

Maintaining Data Integrity

Having an accurate representation of clinical data helps transform discoveries and understanding into patient care and treatment. Centrally-housing data in a compliant environment that enforces data standardization can help clinicians maintain excellent data integrity and provide an authoritative view of their data landscape.

LabKey Server helps maintain data integrity by providing:

  • A highly structured data environment with enforceable data fields to ensure data is entered correctly and within range
  • Quality control measures such as data flags, QC of datasets and built-in QC reports
  • Role and group-based permission levels that allow users only access to what they need access to
  • A compliance module, the allows users to set PHI securities, set Terms of Use for users, and provide electronic signatures on data snapshots

LabKey tools for integrating clinical research dataIntegration of Data from Multiple Sources

Bringing together data from disparate sources into a single system can help clinical research stay on track and on time. Collaborative monitoring of data quality by clinicians, statisticians, and scientists enables quick identification of erroneous data and ensures a reliable, integrated data landscape for comprehensive data analysis.

LabKey Server helps facilitate comprehensive data integration by providing:

  • A study module that can recognize and integrate disparate vendor datasets
  • Built-in and customizable integration with electronic data capture systems and case report forms
  • A clinical document abstraction pipeline, which can extract valuable data from legacy documents

LabKey tools for secure reporting and collaboration in clinical researchSecure Reporting and Collaboration

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

LabKey Server improves reporting and collaboration 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

With the right tools, clinical research teams can eliminate data integration bottle necks and curate reliable datasets for analysis. Sign-up for a free trial to see how LabKey Server can help your team overcome these, and other common clinical research challenges.

Related Documentation

Read more about the features highlighted above on the LabKey Support Portal:

11 Jul 2018
LabKey Server software tools for bench-to-bedside translational research

Bench-to-Bedside: Improving the Feedback Loop

Translational research is making large strides in developing and improving effective agents and therapeutic strategies for patients. Despite these advances, bench-to-bedside and then back to bench science is often hindered by poor data management practices, error-prone manual workflows, and a lack of shared spaces where scientists and clinicians can easily collaborate.

In order to be effective in today’s data-rich research environment, teams need effective software tools to help facilitate the feedback loop between the bench and the bedside. LabKey Server provides essential tools to overcome key bench-to-bedside challenges, including:

LabKey software helps maintain good research recordsMaintenance of Good Research Records

Maintenance of good laboratory records is vital for any research and improves repeatability and reproducibility in experiments.  In translational research, this ultimately leads to improved product development, bringing better treatments from bench to bedside faster.

LabKey Server helps teams maintain good research records by providing:

  • The ability to upload raw assay data and assign metadata, allowing experimental data to be traced back to the original experiment
  • Built-in quality control tools that allow scientists to upload their data and examine it for erroneous values
  • A file watcher that automatically loads new data into a new or existing dataset as it becomes available, reducing human interaction and error, and freeing up time for scientists to focus on the science
  • Compliance tools for signing off on records, ensuring data is reviewed

Integrate laboratory data sources using LabKey software tools

Comprehensive Data Integration

In order to examine the subject comprehensively during treatment, many scientists and clinicians must compile data from multiple sources. This is often time-consuming and slows down research to find better curative agents and therapies.

LabKey Server helps facilitate comprehensive data integration by providing:

  • A compliant study environment with tools that simplify the integration of clinic and research data
  • Automated methods for integrating data from a variety of sources (Flow Cytometry, Luminex, data from Electronic Data Capture systems, etc.)
  • Simplified methods for collecting ad-hoc results
  • Tools for comparing subjects across multiple studies

LabKey software tools for sharing scientific data onlineCollaborative Data Sharing

Sharing data with collaborators improves research, innovation, and ultimately the production of new therapies to help patients. While collaborative data sharing provides significant value in research, hurdles like institutional firewalls and outdated data-sharing methods, like bulky emails and insecure websites, often hinder collaboration in the scientific community.

LabKey Server helps teams collaborate securely by providing:

  • Web-based access to a central platform for data sharing
  • A compliant environment with multi-level permissions, so data sharing is secure
  • The ability to remove PHI fields or randomize IDs when sharing information with collaborators

With the right tools, teams can significantly accelerate the pace of translational research. Sign-up for a free trial to see how LabKey Server can help your team overcome these, and other common research challenges.

Try It Now

The trial version of LabKey Server provides access to many of the platform’s core capabilities, in an easy-to-use hosted environment. Users can explore an example project pre-populated with sample data or create and configure their own LabKey projects according to their research needs.

28 Jun 2018

The Power of Structured Data: Customizing Grid Views in LabKey Biologics

When analyzing the output of an experiment, scientists often need to look beyond the results at related data to answer their research questions. Comparing lineage characteristics like which expression system was used to generate an experiment sample or details about the sample itself, such as the buffer used in it, can uncover crucial data patterns and insights.

This type of data exploration requires data to be captured in a structured manner and integrated into a central system where it can be easily accessed, queried, and analyzed.

Structuring Data for Maximum Value

LabKey Biologics provides tools to ensure that data is correctly structured and consistently stored. For each data type within the LabKey Biologics application, users are able to configure a specific structure, indicating the names of fields as well as their type. Because this data is consistently structured, a user can pull together relevant data from different sources for an integrated view of their data during analysis.

Integrating structured assay and sample data in LabKey Biologics using Sample IDs and look-ups.

For example, when looking at the results for a specific assay type, such as optical density, a user can add details about the samples themselves to the assay results data grid. This might include the buffer used, the expression system used to create it, or the name of the antibody (or other molecule) that was being produced.

Customized Data Views for Quicker Access

Users can customize the default assay data grid view to include these additional look-up columns. Customized default views provide quick access to all the data relevant to the user’s research, instead of having to join data each time they view the dataset. Users can also sort, filter, and search the data in these additional columns the same way they can with native assay data fields.

To see this functionality in action, request a demo! To learn more about LabKey Biologics check out our documentation and resources on the LabKey Support Portal. 

14 Jun 2018
LabKey Server software tools to support basic research data integration and laboratory research management.

Basic Research: Increasing Data Workflows

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:

Connect data from heterogeneous data sourcesEffectively 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

QC checks ensure data integrity and effective integrationEstablishing 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

Secure methods of collaboration on scientific research projectsCollaborative 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 >

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