S. Venkataraman (DCC) talks about the basics of Research Data Management and how to apply this when creating or reviewing a Data Management Plan (DMP). He discusses data formats and metadata standards, persistent identifiers, licensing, controlled vocabularies and data repositories.
link to : dcc.ac.uk/resources
Michigan State University campus policy, resources and best practices for research data management offered by the MSU Libraries Research Data Management Guidance service. http://www.lib.msu.edu/rdmg/
Michigan State University campus policy, resources and best practices for research data management offered by the MSU Libraries Research Data Management Guidance service. http://www.lib.msu.edu/rdmg/
This workshop is meant to be an introduction to the systematic review process. Further information about systematic reviews was available through a research guide. http://libguides.ucalgary.ca/content.php?pid=593664
OpenAIRE webinar: Principles of Research Data Management, with S. Venkatarama...OpenAIRE
The 2019 International Open Access Week will be held October 21-27, 2019. This year’s theme, “Open for Whom? Equity in Open Knowledge,” builds on the groundwork laid during last year’s focus of “Designing Equitable Foundations for Open Knowledge.”
As has become a tradition of sorts, OpenAIRE organises a series of webinars during this week, highlighting OpenAIRE activities, services and tools, and reach out to the wider community with relevant talks on many aspects of Open Science.
An introduction to the FAIR principles and a discussion of key issues that must be addressed to ensure data is findable, accessible, interoperable and re-usable. The session explored the role of the CDISC and DDI standards for addressing these issues.
Presented by Gareth Knight at the ADMIT Network conference, organised by the Association for Data Management in the Tropics, in Antwerp, Belgium on December 1st 2015.
Introduction to research data managementdri_ireland
An Introduction to Research Data Management: slides from a presentation given online on May 12 2022, by Beth Knazook, Project Manager, Research Data. Covers topics such as: what are research data; why share research data; why DMPs are important; and where should you share your data?
This workshop is meant to be an introduction to the systematic review process. Further information about systematic reviews was available through a research guide. http://libguides.ucalgary.ca/content.php?pid=593664
OpenAIRE webinar: Principles of Research Data Management, with S. Venkatarama...OpenAIRE
The 2019 International Open Access Week will be held October 21-27, 2019. This year’s theme, “Open for Whom? Equity in Open Knowledge,” builds on the groundwork laid during last year’s focus of “Designing Equitable Foundations for Open Knowledge.”
As has become a tradition of sorts, OpenAIRE organises a series of webinars during this week, highlighting OpenAIRE activities, services and tools, and reach out to the wider community with relevant talks on many aspects of Open Science.
An introduction to the FAIR principles and a discussion of key issues that must be addressed to ensure data is findable, accessible, interoperable and re-usable. The session explored the role of the CDISC and DDI standards for addressing these issues.
Presented by Gareth Knight at the ADMIT Network conference, organised by the Association for Data Management in the Tropics, in Antwerp, Belgium on December 1st 2015.
Introduction to research data managementdri_ireland
An Introduction to Research Data Management: slides from a presentation given online on May 12 2022, by Beth Knazook, Project Manager, Research Data. Covers topics such as: what are research data; why share research data; why DMPs are important; and where should you share your data?
DataCite – Bridging the gap and helping to find, access and reuse data – Herb...OpenAIRE
OpenAIRE Interoperability Workshop (8 Feb. 2013).
DataCite – Bridging the gap and helping to find, access and reuse data – Herbert Gruttemeier, INIST-CNRS
A North Carolina Connecting to Collections (C2C) workshop co-taught by Audra Eagle Yun (WFU), Nicholas Graham (UNC), and Lisa Gregory (State Archives of NC). This workshop took place on June 13, 2011 in Wilson, NC.
2009 PLANETS Vienna - MIXED migration to XMLDirk Roorda
Snapshot of how we thought about migration infrastructure then: PLANETS for the infrastructure, MIXED as a plugin for the tabular data conversion functionality.
Introduction to Digital Humanities: Metadata standards and ontologies LIBIS
Guest Lecture from Roxanne Wyns (KU Leuven Libraries - LIBIS) given on November 6th 2017. Subject: Introduction to Digital Humanities (B-KUL-G0R03A) for the Master of Digital Humanities: Metadata standards and ontologies.
The need of Interoperability in Office and GIS formatsMarkus Neteler
Free GIS and Interoperability: The need of Interoperability in Office and GIS formats
GIS Open Source, interoperabilità e cultura del dato nei SIAT della Pubblica Amministrazione
[GIS Open Source, interoperability and the 'culture of data' in the spatial data warehouses of the Public Administration]
OAIS and It's Applicability for Libraries, Archives, and Digital Repositories...faflrt
ALA/FAFLRT Workshop on Open Archival Information Service (OAIS). Presented by Robin Dale, RLG. Sponsored by ALA Federal and Armed Forces Libraries Roundtable (FAFLRT). Presented on June 16, 2001 at the ALA Annual Conference.
Started in 2004 (under ASTM Committee E13.15) the Analytical Information Markup Language (AnIML) is an XML based standard for capturing, sharing, viewing, and archiving analytical instrument data from any analytical technique.
This paper discusses the AnIML standard in terms of philosophy, structure, usage, and the resources available to work with the standard. Examples will be given for different techniques as well as strategies for migration of legacy data. Finally, the current status of the standard and time frame for promulgation through ASTM will be reported.
Site up an open access-ICAR
Institutional Repository-Hardware, Software, Policies and Personnel.
ICAR Initiatives
Under NATP Project – Integrated National Agricultural Resources Information System INARIS (Rai et. Al., 2007). A Central Data warehouse (CWD) of agricultural resources was established at IASRI
This project having collaborations with 13 other organizations of ICAR.
In this view 13 different data marts were designed.
This Project was available under this link (http://agdw.iasri.res.in)
My outlook Country should have agri-search engine
Agri-Search Engine should be developed in country to aggregate information from the internet and provide it to farmers in meaningful manner through using ICT tools.
Agri-Search Engine be coordinated with Govt. of India’s Agricultural Websites to monitor each website per day.
OpenAIRE Content Providers Community Call, November 4th, 2020
This call was focused on the PROVIDE future developments, functionalities wishlist and PROVIDE service in EOSC.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Recordings: https://youtu.be/wY4fOS767Us
Follow the Community activities at https://www.openaire.eu/provide-community-calls
OpenAIRE in the European Open Science Cloud (EOSC)OpenAIRE
Openness is the success factor for EOSC. OpenAIRE has been working in delivering an open access scholarly communication in Europe for the past 10 years and we now present how our work fits into the EOSC core developments
OpenAIRE Content Providers Community Call, October 7th, 2020
This call was focused on the OpenAIRE Broker Service, specifying how the service works to deploy the enrichment events to the Content Providers managers.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Recording: https://youtu.be/3sF4B58EGcs
Follow the Community activities at https://www.openaire.eu/provide-community-calls
OpenAIRE Content Providers Community Call, July 1st, 2020
This call was focused on Data Repositories namely the OpenAIRE Research Graph and Data Repositories, the OpenAIRE Content Acquisition Policy, and the Guidelines for Data Archive Managers.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Follow the Community activities at https://www.openaire.eu/provide-community-calls
OpenAIRE Content Providers Community Call. May 6th, 2020.
This Call focused the presentation of the new User Interface of Provide Dashboard and the presentation of 4 use cases using the Provide service.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Recording available here: https://youtu.be/J4m_ryRxtnY
20200504_OpenAIRE Legal Policy Webinar: GDPR and Sharing DataOpenAIRE
Presentation by Jacques Flores Dourojeanni (Research Data Management Consultant Utrecht University Library), as delivered during the OpenAIRE Legal Policy Webinar series on May 4th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200504_Research Data & the GDPR: How Open is Open?OpenAIRE
Presentation by Prodromos Tsiavos (Senior Legal Advisor - ARC/ Director - Onassis Group) as delivered during the OpenAIRE Legal Policy Webinar series on May 4th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200504_Data, Data Ownership and Open ScienceOpenAIRE
Presentation by Thomas Margoni (Senior Lecturer in Intellectual Property and Internet Law, Co-director, CREATe, University of Glasgow) as delivered during the OpenAIRE Legal Policy Webinar series on May 4th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200429_Research Data & the GDPR: How Open is Open? (updated version)OpenAIRE
Presentation by Prodromos Tsiavos (Senior Legal Advisor - ARC/ Director - Onassis Group) as delivered during the OpenAIRE Legal Policy Webinar series on April 29th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200429_Data, Data Ownership and Open ScienceOpenAIRE
Presentation by Thomas Margoni (Senior Lecturer in Intellectual Property and Internet Law, Co-director, CREATe, University of Glasgow) as delivered during the OpenAIRE Legal Policy Webinar series on April 29th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200429_OpenAIRE Legal Policy Webinar: GDPR and Sharing DataOpenAIRE
Presentation by Jacques Flores Dourojeanni (Research Data Management Consultant Utrecht University Library), as delivered during the OpenAIRE Legal Policy Webinar series on April 29th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
COVID-19: Activities, tools, best practice and contact points in GreeceOpenAIRE
Presentation from the webinar organized by the Greek OpenAIRE and RDA Nodes (Athena RC) and Elixir-GR to inform participants of EU and national efforts, in collaboration with the following research organizations: Flemming, CERTH, HEAL-Link, Demokritos, Univ. of Athens (Medical School).
Presentation of the 2nd Content Providers Community Call, targeting the following topics: 1) OpenAIRE Content provider dashboard updates; Main topic: DSpace-CRIS for OpenAIRE: implementation of the CRIS guidelines and beyond; 3) Community questions & comments.
Presentation of the 2nd Content Providers Community Call, targeting the following topics: 1) OpenAIRE Content provider dashboard updates;
2) OpenAIRE aggregation and enrichment processes: specifications and good practices;
3) Community questions & comments.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
1. Basics in good research data
management (RDM) for
reviewing DMPs
FOSTER & OpenAIRE webinar, 22nd October 2018
https://www.openaire.eu/open-access-week-2018
S. Venkataraman
Digital Curation Centre, Edinburgh
s.venkataraman@ed.ac.uk
https://doi.org/10.5281/zenodo.1461601
3. What is Research Data Management?
Create
Document
Use
Store
Share
Preserve
“the active management
and appraisal of data
over the lifecycle of
scholarly and scientific
interest”
Data management is
part of
good research
practice
4.
5. Concepts to cover
•Data formats
•Metadata
•Licensing
•Data repositories
•Persistent identifiers
These aspects are addressed specifically in Data Management Plans so here
we will help you review them
7. Data Formats
Different formats are good for different things
- open, lossless formats are more sustainable e.g. rtf, xml, tif, wav
- proprietary and/or compressed formats are less preservable but are
often in widespread use e.g. doc, jpg, mp3
One format for analysis then convert to a standard format
Data centres may suggest preferred formats for deposit
https://www.ukdataservice.ac.uk/manage-data/format/recommended-
formats
8. Data Formats
Type of data Recommended formats Acceptable formats
Tabular data with extensive metadata
variable labels, code labels, and defined missing values
SPSS portable format (.por)
delimited text and command ('setup') file (SPSS, Stata, SAS, etc.)
structured text or mark-up file of metadata information, e.g. DDI XML file
proprietary formats of statistical packages: SPSS (.sav), Stata (.dta), MS
Access (.mdb/.accdb)
Tabular data with minimal metadata
column headings, variable names
comma-separated values (.csv)
tab-delimited file (.tab)
delimited text with SQL data definition statements
delimited text (.txt) with characters not present in data used as delimiters
widely-used formats: MS Excel (.xls/.xlsx), MS Access (.mdb/.accdb), dBase
(.dbf), OpenDocument Spreadsheet (.ods)
Geospatial data
vector and raster data
ESRI Shapefile (.shp, .shx, .dbf, .prj, .sbx, .sbn optional)
geo-referenced TIFF (.tif, .tfw)
CAD data (.dwg)
tabular GIS attribute data
Geography Markup Language (.gml)
ESRI Geodatabase format (.mdb)
MapInfo Interchange Format (.mif) for vector data
Keyhole Mark-up Language (.kml)
Adobe Illustrator (.ai), CAD data (.dxf or .svg)
binary formats of GIS and CAD packages
Textual data Rich Text Format (.rtf)
plain text, ASCII (.txt)
eXtensible Mark-up Language (.xml) text according to an appropriate
Document Type Definition (DTD) or schema
Hypertext Mark-up Language (.html)
widely-used formats: MS Word (.doc/.docx)
some software-specific formats: NUD*IST, NVivo and ATLAS.ti
Image data TIFF 6.0 uncompressed (.tif) JPEG (.jpeg, .jpg, .jp2) if original created in this format
GIF (.gif)
TIFF other versions (.tif, .tiff)
RAW image format (.raw)
Photoshop files (.psd)
BMP (.bmp)
PNG (.png)
Adobe Portable Document Format (PDF/A, PDF) (.pdf)
Audio data Free Lossless Audio Codec (FLAC) (.flac) MPEG-1 Audio Layer 3 (.mp3) if original created in this format
Audio Interchange File Format (.aif)
Waveform Audio Format (.wav)
Video data MPEG-4 (.mp4)
OGG video (.ogv, .ogg)
motion JPEG 2000 (.mj2)
AVCHD video (.avchd)
Documentation and scripts Rich Text Format (.rtf)
PDF/UA, PDF/A or PDF (.pdf)
XHTML or HTML (.xhtml, .htm)
OpenDocument Text (.odt)
plain text (.txt)
widely-used formats: MS Word (.doc/.docx), MS Excel (.xls/.xlsx)
XML marked-up text (.xml) according to an appropriate DTD or schema, e.g.
XHMTL 1.0
10. Metadata and documentation
At a basic level, metadata supports data discovery, disambiguation and
citation
Rich metadata and documentation will support interoperability & reuse
Standards should be used. These can be general – such as Dublin Core, or
discipline specific
Data Documentation Initiative (DDI) – social science
Ecological Metadata Language (EML) - ecology
Flexible Image Transport System (FITS) – astronomy
11. Where to find relevant standards?
Metadata Standards Directory
Broad, disciplinary listing of
standards and tools. Maintained
by RDA group
https://rdamsc.dcc.ac.uk
FAIRsharing
•A portal of data standards, databases,
and policies
•Focused on life, environmental and
biomedical sciences, but expanding to
other disciplines
https://fairsharing.org
12. Value of controlled vocabularies
“MTBLS1: A metabolomic study of urinary changes in type 2 diabetes in……”
Example courtesy of Ken Haug, European
Bioinformatics Institute (EMBL-EBI)
13. Controlled vocabularies
• e.g. SNOMED CT (clinical terms) or MeSH
• Include ontologies as well
• Defined terms + taxonomy
• Useful for selecting keywords to tag datasets
• Example: compare anatomical components in two distinct species of organism…
➢Organism A
➢Term A1
➢Term A2
➢Term A3
➢Term B1
➢Term B2
➢Term C4
➢.
➢.
➢.
➢Term n
►Organism B
►Term A1
►Term A2
►Term A3
►Term B1
►Term B2
►Term C4
►.
►.
►.
►Term n
18. Data repositories
www.re3data.org
The EC guidelines point to Re3data as one of the registries that can be
searched to find a home for data
www.fosteropenscience.eu/content/re3data-demo
19. Considerations when selecting repositories
• Often preferable to use a subject specific repository if available
• Useful if repositories assign a persistent identifier
• Look for certification as a ‘Trustworthy Digital Repository’ with an explicit
ambition to keep the data available in long term.
• Generic repositories are also available e.g. Zenodo or institutional
repositories Icons to note
open access,
licenses, PIDs,
certificates…
21. Persistent Identifiers
• a long-lasting reference to a document, file or other object
• PIDs come in various forms e.g. ARK, DOI, URN, PURL, Handles...
• Typically they’re actionable i.e. type it into web browser to access
• Many repositories will assign them on deposit
22. Persistent Identifiers
A specific example: ORCID
https://orcid.org/blog/2017/10/04/building-information-infrastructure-
research-institutions
https://orcid.org/blog/2016/10/31/organization-identifier-project-way-
forward
23. Thanks for watching!
More info at:
www.dcc.ac.uk/resources/
https://www.fosteropenscience.eu/
https://www.openaire.eu/