Survey on LIMS used in mouse phenotyping facilities

There are many different definitions for the term 'LIMS'. When we are talking about LIMS in this questionnaire, we mean generation of worksheets and worklists, workload management, sample management, phenotyping data capture, manual or automatic results entry, result data management, standard report generation as well as data visualisation and data analysis.

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1. Your name and details

Your name and details Full name
E-mail
Position
Institution
Department
City
Country
Name of the animal facility you are reporting on (to identify the animal facility subunit your answer corresponds to)

2. Looking at the mice living in your facility, to which research areas do the phenotyping procedures carried out on them belong to?

Looking at the mice living in your facility, to which research areas do the phenotyping procedures carried out on them belong to? Behavior

Neurology and sensory system

Nociception

Eye and vision

Immune system

Clinical chemistry

Nutrition and nutrigenomics

Hormone system

Metabolomics

Energy metabolism

Anatomy and morphology

Developmental biology

Bone and cartilage

Cardiovascular function

Angiogenesis

Lung function

Bio-imaging

Disease-oriented research using mice as model organisms for human disease

Functional genomics

Gene expression

Proteomics

Transcriptomics

Radiation biology

Toxicology

Pathology

Carcinogenesis

Exploring the function of other organs not mentioned above

General animal husbandry and animal welfare

Drug development

Studies on longevity and aging

Fertility

Microbiology, viruses, parasites and infectious diseases

Gut flora

Challenge tests

Other (please specify)

3. Where or how do you store parametric phenotyping results (i.e. metric, text, boolean, categorial, ordinal data)?

Where or how do you store parametric phenotyping results (i.e. metric, text, boolean, categorial, ordinal data)? In a lab journal

In files such as MS Excel or MS Word

In desktop databases (such as MS Access or Filemaker)

In central relational databases (such as Oracle, PostgreSQL, DB/2, MySQL, Sybase, etc.) connected to software applications

Other (please specify)

4. If you use a database-driven software application for the management of phenotyping results, please describe the software

If you use a database-driven software application for the management of phenotyping results, please describe the software Web-based system that runs in a browser on the client computer

Application that runs on a terminal server

Stand-alone application (access from only one client computer at any given time, no concurrent write access)

Java applet or servlet

Other (please specify)

5. Technical aspects of your LIMS (please enter 'n/a' if a question cannot be answered):

Technical aspects of your LIMS (please enter 'n/a' if a question cannot be answered): Data storage: database or spreadsheet application used
Programming language(s) / framework(s) used
Architecture (n-tier, web application …)
Supported operating systems of server
Supported operating systems of client computers
Natural language of the graphical user interface
Natural language of the database table definitions
Comments

6. On which level can your LIMS store phenotyping results?

On which level can your LIMS store phenotyping results? On the level of individual mice: phenotyping results are assigned to single mice

Typical phenotype of a group of mice (composed by the user)

Typical phenotype of a mutant mouse line

Typical phenotype of a genetic background

7. How are results transfered from the analysing device (that captures the phenotyping raw data) into your LIMS?

How are results transfered from the analysing device (that captures the phenotyping raw data) into your LIMS? We key them into a flat file, from there the values can be extracted

We enter them into the database by using forms on the graphical user interface of the LIMS

The analysing software stores results in a flat file, from there the values can be extracted

The analysing software stores results in a result database, from there the values can be extracted

The results are directly transferred from the analysing device into the LIMS without any steps of human intervention

Other (please specify)

8. What are your data upload policies?

What are your data upload policies? We upload all results and flag results later if they are not valid

We report why results are not regarded as being valid

We report the reason of missing values

We first validate our results and then upload valid results only

We upload calibration results as well

We upload quality control results as well

Results are checked for plausibility before the upload using custom-made rules (e.g. definition of minimum and maximum for numeric values)

Results are checked for plausibility by a data curator after upload

Other (please specify)

9. How does your LIMS store phenotyping results?

How does your LIMS store phenotyping results? Free text

Local custom-made controlled vocabulary

Broadly accepted (phenotype) ontology, such as Mammalian Phenotype Ontology or Entity/ Quality ontology

Ontology terms on the level of single mice

Ontology terms on the level of mutant mouse lines / strains

Parametric results

Annotations for images and videos

If you use ontologies, please name the ones you use

10. How many single phenotyping results are approximately stored in your LIMS (i. e. results of the examination of one mouse and one phenotyping parameter)?

How many single phenotyping results are approximately stored in your LIMS (i. e. results of the examination of one mouse and one phenotyping parameter)? < 10.000

10.000 – 50.000

50.000 – 200.000

200.000 – 500.000

500.000 – 1.000.000

> 1.000.000

Comment

In the next questions, the term 'raw data' is used. In this context, raw data means the measured value or the phenotypic observation, which in many cases still has to be converted using a calibration curve (e.g. for photometric analysis) or has to be standardised by relating a value to the body weight to form the final value for further statistical data analysis.

11. Do you store raw data in a central database?

Do you store raw data in a central database? Yes, all kind of results (including raw data) are stored in a central database

No, only final and validated results are stored in a central database

We don't use a central database for results at all, but we store raw data in flat files outside the database

Final results are stored in a database, raw data are stored separately on client computers or on a network server

Other (please specify)

12. Which of the following statements regarding storage of large size mouse images (from CT, x-ray, PET, MRI, etc.) or other large files are true for your facility?

Which of the following statements regarding storage of large size mouse images (from CT, x-ray, PET, MRI, etc.) or other large files are true for your facility? They are stored as distinct files on hard disks of client computers

They are stored as distinct files on a central file server

Only stable file system links (URIs) are stored in the database

They are stored as binary large objects in a database

There is a backup strategy for these files to prevent data loss

The files are stored on a RAID server to reduce risk of data loss

No backups are made because of storage capacity reasons

Images from finished projects are archived on different storage media

The files are directly linked to the corresponding mouse / mice

The files can be opened and viewed from the LIMS

In our LIMS the files are not linked to the corresponding mouse

We don't generate these kinds of large files in our facility

Other (please specify)

13. Are your animal husbandry management system and your LIMS inseparably connected or could they run independently as well?

Are your animal husbandry management system and your LIMS inseparably connected or could they run independently as well? They are both part of a united management system and hence cannot run independently

They could / do run independently

We use paper or flat files for both purposes

Other (please specify)

14. In your LIMS, do you assign a unique sample identifier to any kind of samples?

In your LIMS, do you assign a unique sample identifier to any kind of samples? Yes

15. Can you manage samples from animals that were not housed in your animal facility but came from external collaboration partners?

Can you manage samples from animals that were not housed in your animal facility but came from external collaboration partners? Yes, samples from external mice not having an internal unique mouse identifier can be handled and the results can be stored in our LIMS

Yes, we can analyse these samples by using dummy sample identifier

Yes, we can analyse these samples, but the results will not be stored in our LIMS

No, samples from external mice cannot be handled, only samples from mice living in our animal facility

We don't analyze samples from external mice at all

Other (please specify)

16. Do you store date and time of a measurement for any phenotyping procedure performed on a mouse?

Do you store date and time of a measurement for any phenotyping procedure performed on a mouse? No, we don't report date or time at all

No, we report the day of measurement only

No, we do report date and time, but not on the level of individual mice, but the starting date / time when a cohort of mice was measured

No, we report date and time for some assays only

No, we report the age of the mouse at the day of measurement

Yes, we store date and time for every measurement

Other (please specify)

17. Do you report metadata describing the experimental or environmental conditions during the measurement (such as reagent lot numbers, analyzing devices used, technician who performed the procedure, room temperature, diet, results of quality controls etc.) which might be relevant for the outcome?

Do you report metadata describing the experimental or environmental conditions during the measurement (such as reagent lot numbers, analyzing devices used, technician who performed the procedure, room temperature, diet, results of quality controls etc.) which might be relevant for the outcome? Yes, we report experimental conditions

Yes, we report environmental conditions

Yes, we report other metadata

No, we don't report metadata at all

Other (please specify)

18. Have you ever transferred phenotyping results from your LIMS into a public database in a standardised format? If yes, into which database?

Have you ever transferred phenotyping results from your LIMS into a public database in a standardised format? If yes, into which database? No, we haven't done so, but we might do it in the future

No, we won't upload results into public databases

Yes, we've uploaded results into the Mouse Phenome Database

Yes, we've uploaded results into the EuroPhenome database

Yes, we've uploaded results into the EMMA database

Yes, we've uploaded results into some other public database (not mentioned above) before

Other public databases (please specify)

19. Do collaboration partners have access to phenotyping results stored in your LIMS?

Do collaboration partners have access to phenotyping results stored in your LIMS? Yes, a web-based access is possible

No, external access to the data for collaboration partners is not possible

No, we send a report of our findings only

20. Can you give an overall rating of your satisfaction with the current LIMS solution?

	1 - very good	2 - good	3 - good enough	4 - not sufficient	5 - inacceptable
Functionality	*Can you give an overall rating of your satisfaction with the current LIMS solution? Functionality 1 - very good	Functionality 2 - good	Functionality 3 - good enough	Functionality 4 - not sufficient	Functionality 5 - inacceptable
Reliability	Reliability 1 - very good	Reliability 2 - good	Reliability 3 - good enough	Reliability 4 - not sufficient	Reliability 5 - inacceptable
Speed	Speed 1 - very good	Speed 2 - good	Speed 3 - good enough	Speed 4 - not sufficient	Speed 5 - inacceptable
Intuitive use	Intuitive use 1 - very good	Intuitive use 2 - good	Intuitive use 3 - good enough	Intuitive use 4 - not sufficient	Intuitive use 5 - inacceptable
Flexibility	Flexibility 1 - very good	Flexibility 2 - good	Flexibility 3 - good enough	Flexibility 4 - not sufficient	Flexibility 5 - inacceptable
Scalability	Scalability 1 - very good	Scalability 2 - good	Scalability 3 - good enough	Scalability 4 - not sufficient	Scalability 5 - inacceptable
Quality control	Quality control 1 - very good	Quality control 2 - good	Quality control 3 - good enough	Quality control 4 - not sufficient	Quality control 5 - inacceptable

Other (please specify)

21. How do you perform statistical analysis and data visualisation on your phenotyping results?

How do you perform statistical analysis and data visualisation on your phenotyping results? We've added custom functions into our LIMS software

Our LIMS has an interface for data transfer to an independent statistics software (such as SAS, R, SPSS, etc.)

Result analysis and visualisation take place exclusively outside our LIMS

A statistics and/or visualisation software tool is integrated into our LIMS

We use standard office software such as MS Excel for visualisation

22. How do you tag "interesting" phenotyping results in your LIMS?

How do you tag "interesting" phenotyping results in your LIMS? Our users have to find out interesting data themselves and tag these results manually

An automated job identifies interesting data by applying certain statistical methods or custom-defined rules

Not at all

23. If your LIMS is a database-driven software application, where was it developed and is it available for others as well?

If your LIMS is a database-driven software application, where was it developed and is it available for others as well? It was developed in-house and customized to our facility and needs

It was developed by a different academic institution

It was developed and custom-maded by a company

It was developed by a company and licensed without any adaptations

You can buy user licenses from a company

It is offered for free without access to the source code

It is offered for free with access to the source code (i.e. as open-source software)

It is not offered to anyone else

Comments

24. Do you have any recommendations for institutions establishing a new mouse facility from scratch on what they should pay attention to (concerning informatics aspects)?

Do you have any recommendations for institutions establishing a new mouse facility from scratch on what they should pay attention to (concerning informatics aspects)?

25. Please use the space below for any kind of comments on the survey or anything else you want to tell us:

Please use the space below for any kind of comments on the survey or anything else you want to tell us:

Survey on LIMS used in mouse phenotyping facilities

*1. Your name and details

2. Looking at the mice living in your facility, to which research areas do the phenotyping procedures carried out on them belong to?

3. Where or how do you store parametric phenotyping results (i.e. metric, text, boolean, categorial, ordinal data)?

4. If you use a database-driven software application for the management of phenotyping results, please describe the software

5. Technical aspects of your LIMS (please enter 'n/a' if a question cannot be answered):

6. On which level can your LIMS store phenotyping results?

7. How are results transfered from the analysing device (that captures the phenotyping raw data) into your LIMS?

8. What are your data upload policies?

9. How does your LIMS store phenotyping results?

10. How many single phenotyping results are approximately stored in your LIMS (i. e. results of the examination of one mouse and one phenotyping parameter)?

11. Do you store raw data in a central database?

12. Which of the following statements regarding storage of large size mouse images (from CT, x-ray, PET, MRI, etc.) or other large files are true for your facility?

13. Are your animal husbandry management system and your LIMS inseparably connected or could they run independently as well?

14. In your LIMS, do you assign a unique sample identifier to any kind of samples?

15. Can you manage samples from animals that were not housed in your animal facility but came from external collaboration partners?

16. Do you store date and time of a measurement for any phenotyping procedure performed on a mouse?

17. Do you report metadata describing the experimental or environmental conditions during the measurement (such as reagent lot numbers, analyzing devices used, technician who performed the procedure, room temperature, diet, results of quality controls etc.) which might be relevant for the outcome?

18. Have you ever transferred phenotyping results from your LIMS into a public database in a standardised format? If yes, into which database?

19. Do collaboration partners have access to phenotyping results stored in your LIMS?

20. Can you give an overall rating of your satisfaction with the current LIMS solution?

21. How do you perform statistical analysis and data visualisation on your phenotyping results?

22. How do you tag "interesting" phenotyping results in your LIMS?

23. If your LIMS is a database-driven software application, where was it developed and is it available for others as well?

24. Do you have any recommendations for institutions establishing a new mouse facility from scratch on what they should pay attention to (concerning informatics aspects)?

25. Please use the space below for any kind of comments on the survey or anything else you want to tell us:

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1. Your name and details