STRENDA is an organization that aims to standardize the reporting of enzymology data through three main missions: 1) Standardizing experimental conditions, 2) Defining minimum information that must be reported for enzyme functional data, and 3) Defining requirements for submitting uniform functional data through an "e-form". The organization was founded in 2004 and is supported by the Beilstein-Institut. It works to ensure comprehensive and consistent reporting of materials, methods, and results in publications.
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Pre-processing with outlier detection,
denoising and analysis using deep learning
Alternative download link:
https://www.dropbox.com/s/nvp70vyslvggte1/PLR_overview.pdf?dl=0
This poster by Mary Shimoyama about RGD's PhenoMiner Phenotype Database and Data Mining tool was presented at the December 2009 Rat Genomics and Models meeting at Cold Spring Harbor Laboratory.
Data Management for Quantitative Biology - Data sources (Next generation tech...QBiC_Tue
Introduction to next generation sequencing (NGS); NGS data; data management of NGS data; third generation sequencing; NGS pipelines; NGS experimental design
Talk given at the symposium about government-funded databases and open chemistry at the national meeting of the American Chemical Society in Washington, 21 Aug 2017
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024dkNET
Presenter: Sanchita Bhattacharya, ImmPort Science Program Lead, Bakar Computational Health Sciences Institute UCSF
Abstract
The Immunology Database and Analysis Portal (ImmPort, https://www.immport.org/home) is a domain-specific data repository for immunology-related data which is funded by the National Institutes of Health, National Institute of Allergy and Infectious Diseases, and Division of Allergy, Immunology, and Transplantation. ImmPort has been making scientific data Findable, Accessible, Interoperable, and Reusable (FAIR) for over 20 years. ImmPort data sets encompass over 7 million experimental results across 160 diseases and conditions, including data related to diabetes, kidney and liver transplantation, celiac disease, and many more conditions. In this webinar, participants will learn about data management and sharing through ImmPort, as well as finding and leveraging data sets of interest for research.
The top 3 key questions that the ImmPort can answer:
1. How can researchers share data through ImmPort to comply with the NIH Data Management and Sharing policy?
2. How does ImmPort support FAIR data and why is this powerful for research?
3. What scientific data does ImmPort house that would be of interest to NIDDK researchers?
Upcoming webinars schedule: https://dknet.org/about/webinar
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Pre-processing with outlier detection,
denoising and analysis using deep learning
Alternative download link:
https://www.dropbox.com/s/nvp70vyslvggte1/PLR_overview.pdf?dl=0
This poster by Mary Shimoyama about RGD's PhenoMiner Phenotype Database and Data Mining tool was presented at the December 2009 Rat Genomics and Models meeting at Cold Spring Harbor Laboratory.
Data Management for Quantitative Biology - Data sources (Next generation tech...QBiC_Tue
Introduction to next generation sequencing (NGS); NGS data; data management of NGS data; third generation sequencing; NGS pipelines; NGS experimental design
Talk given at the symposium about government-funded databases and open chemistry at the national meeting of the American Chemical Society in Washington, 21 Aug 2017
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024dkNET
Presenter: Sanchita Bhattacharya, ImmPort Science Program Lead, Bakar Computational Health Sciences Institute UCSF
Abstract
The Immunology Database and Analysis Portal (ImmPort, https://www.immport.org/home) is a domain-specific data repository for immunology-related data which is funded by the National Institutes of Health, National Institute of Allergy and Infectious Diseases, and Division of Allergy, Immunology, and Transplantation. ImmPort has been making scientific data Findable, Accessible, Interoperable, and Reusable (FAIR) for over 20 years. ImmPort data sets encompass over 7 million experimental results across 160 diseases and conditions, including data related to diabetes, kidney and liver transplantation, celiac disease, and many more conditions. In this webinar, participants will learn about data management and sharing through ImmPort, as well as finding and leveraging data sets of interest for research.
The top 3 key questions that the ImmPort can answer:
1. How can researchers share data through ImmPort to comply with the NIH Data Management and Sharing policy?
2. How does ImmPort support FAIR data and why is this powerful for research?
3. What scientific data does ImmPort house that would be of interest to NIDDK researchers?
Upcoming webinars schedule: https://dknet.org/about/webinar
1. STRENDA
MIBBI Workshop 2010
= Standards for Reporting Enzymology Data
The Commission:
R. Armstrong, A. Bairoch, A. Cornish-Bowden, P. Halling, J. Rohwer,
T. Leyh, K. Tipton, D. Schomburg, C. Steinbeck and C. Kettner (co-ordination)
Missions:
1. Standardized experimental conditions*;
2. Definition of minimum information for reporting enzyme
functional data (“STRENDA Guidelines”);
3. Definition of requirements for the submission of uniform
functional data (“STRENDA e-form”).
Founded and supported by the Beilstein-Institut since 2004
www.strenda.org
Accompanied by Int‘l Symposia on ESCEC (next Sept. 2011)
* Van Eunen et al. (2010) FEBS J. 277(3):749-760
2. Minimum Information…
…about experimental set up.
…about materials and methods used.
…about data obtained.
e.g., identity and source of enzyme, description of reaction…
e.g. use of kinetic param. units,
determination of params.,
inhibition and activation, statistics…
MIBBI Workshop 2010* http://www.beilstein-institut.de/STRENDA/eform/eform.html
…for the STRENDA
„e-form“ *
e.g., preparation of enzyme, experimental
conditions, methodology of assay,…
… for capturing uniform enzyme data.
Publication of materials, methods
and results comprehensively.
4. http://www.beilstein-institut.de/en/projects/strenda/
The Commission: Richard Armstrong, Vanderbilt Univ., Nashville, TN, USA
Amos Bairoch, SBI, Geneva, Switzerland
Athel Cornish-Bowden, CNRS-BIP, Marseille, France
Peter Halling, Univ. of Strathclyde, Glasgow, UK
Johann Rohwer, Univ. of Stellenbosch, South Africa
Tom Leyh, The Albert Einstein College, New York, USA
Keith Tipton, Trinity College, Dublin, Ireland
Dietmar Schomburg, Technical University of Braunschweig
Christoph Steinbeck, EBI, Cambridge, UK
Carsten Kettner, Beilstein-Institut, Frankfurt
STRENDA
There was a young lady called BRENDA
And I tried to find data to send her
But she says "It's no good,
And I think that you should
Send me stuff that's consistent with STRENDA
(Athel Cornish-Bowden, Feb. 2004)
5. There was a young lady called BRENDA
And I tried to find data to send her
But she says "It's no good,
And I think that you should
Send me stuff that's consistent with STRENDA
(Athel Cornish-Bowden, Feb. 2004)
Editor's Notes
STRENDA stands for Standards for Reporting Enzymology Data and the Commission has been founded in 2004 under the auspices of the Beilstein-Institut and is supported since then.
The Commission work is accompanied by the biannually held ESCEC Symposia. The next symposium will be in September 2011.
At the first Symposium on ESCEC there was a common agreement that standardized descriptions of materials, methods and results for enzymology experiments are desired and useful.
With this idea of the establishment of standards for reporting minimum information, the STRENDA Commission took over to address the following issues.
to propose standardized assay conditions
This issue has just been tackled when standard assay conditions for the functional characterization of the yeast glycolysis enzymes were developed and tested.
to define minimal information for reporting enzyme functional data
to define the requirements for the deposition of such data in a form that will be available to any relevant database.
For a high degree of comparability, enzymology in basic research relies in a first step data which include minimum experimental information.
about the experimental set up which includes also description of the methodology,
about the materials and methods used such as enzyme information, preparation, assay condition etc.,
and about the data obtained which means information about measured kinetic parameters and mechanisms, inhibition and activation parameters and so on.
Capturing Uniform Enzyme Data
The third goal is the development of a comprehensive data acquisition and storage system in compliance with the STRENDA guidelines.
This system is proposed to act as a portal for the submission of enzyme data prior or during publication to a freely accessible, public database. The prototype is accessible here for a community-wide evaluation. We have already received numerous comments and suggestions for this project which will be considered at the following development steps.
We hope that both the guidelines and data acquisition system will lead to the publication and storage of materials, methods and results in a comprehensive way.
Due to the efforts of the members of STRENDA the network of co-operations, collaborations and contacts is continuously growing:
in 2005 JCBN approved the guidelines at the annual NC-IUBMB meeting (International Union of Biochemistry and Molecular Biology),
close contacts to YSBN and the NIH Chemical Genomics Center as well as to department of Biotechnology and Enzyme Catalysis and Regulation at the National Institute of
General Medical Sciences
STRENDA is registered at the MIBBI project since 2007.
More or less incidentally the European Section of Applied Biocatalysis, a subsection of the European Federation of Biotechnolgy, became aware of the STRENDA guidelines and
the members of this working group decided to adopt the STRENDA guidelines for their purposes.
So, who will be next? Any input, cooperation and contribution are highly appreciated
The major database producers in the enzyme field are also closely connected with STRENDA. SABIO-RK implements the recommendations of the STRENDA commission.
The STRENDees appreciated that a number of journals have already adopted the guidelines for their instructions for authors, amongst them are FEBS J., Biochemistry, JBC,
ABB, BBRC and all nine sections of BBA, Nature Chemical Biology entered recently and FEBS Letters will follow soon.
Up to date, 15 biochemical journals have already adopted the STRENDA Guidelines for their instructions for authors.
BMC, PLoS and OMICS recommend the authors to the MIBBI portal for prescriptive checklists for reporting their research data.
So we hope that further journals will follow.