Resea ch Da a Managemen
(RDM)
Ma in Bole
P epa ed in acco dance wi h NFDI4Mic obio a, unded by DFG
Sou ce ma e ial: NFDI4Mic obio a - Knowledge Base (CC-BY)
Con en s
1. De ini ion o Resea ch Da a and Resea ch Da a Managemen (RMD)
2. FAIR da a p inciples
3. Da a Managemen Plans (DMPs)
2
Wha is Resea ch Da a Managemen ?
Resea ch Da a Managemen (RDM)
“A se ies o measu es ha need o be aken du ing a esea ch p ojec in
o de o ob ain high-quali y da a (whe he p oduced o eused) ¹ , make da a ⁽ ⁾
a ailable and usable o e he long- e m ² , and make esea ch indings ⁽ ⁾
ep oducible beyond he esea ch p ojec ³ “⁽ ⁾
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Resea ch Da a Li e Cycle
¹ Resea ch Da a. h ps:// ii.de/en/ opics/# o schungsda en
² B es, E., Rudol , D., Linds äd , B., & Shu sko, A. (2022). Resea ch Da a Managemen in Medical and Biomedical Sciences.
³ Voigh , P., F e icks, S., Linds äd , B., Shu sko, A., & Vandendo pe, J. (2022). Wo kshop on Resea ch Da a.
Resea ch Da a Managemen (RDM)
Es ablishing clea p o ocols o :
-Da a collec ion and gene a ion (SOPs - S anda d Ope a ing P ocedu es)
-Da a s o age (p e e ably public eposi o ies like ENA, NCBI, DDBJ)
-Da a analysis (wo k low, pipeline, so wa e e sioning, models used)
-S anda dized da a o ma s (FASTA, FASTQ, GenBank, .cs , . s , e c.)
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Resea ch (me a)da a
Resea ch (me a)da a
De ini ion a ies ac oss disciplines and esea ch unding agencies
“Any in o ma ion collec ed, s o ed, and p ocessed o p oduce and alida e
o iginal esea ch esul s “
(DeWi Wallace Lib a y; h ps://libguides.macales e .edu/da a1)
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Da a Types
Common ypes o da a in mic obiology
In mic obiology, se e al di e en ypes o da a exis , all o hem impo an o unde s and some pa o he, dynamic, unc ion, s uc u e
o a mic obial communi y o i s indi idual ep esen a i es. All o hem ep esen a di e en laye o in o ma ion.
Common ypes o da a in mic obiology:
-Genomic sequences,
-Amplicon sequences,
-Me agenomic sequences,
-Me agenome Assembled Genome (MAG) sequences,
-(Me a) ansc ip omic sequences,
-(Me a)p o eomic da a,
-Me abolomic da a.
Types o me ada a
Technical me ada a e e s o he echnical pa o da a gene a ion and p ocessing:
●Ins umen a ion and Pla o ms Used
●Sample Collec ion and Handling P ocedu es
●Sample P epa a ion and Ex ac ion P o ocols
●So wa e Tools and Ve sions U ilized o Da a P ocessing
En i onmen al/Biological me ada a e e s o he con ex o sample collec ion:
●Ecosys em o Habi a In o ma ion
●En i onmen al Condi ions (e.g., pH, salini y, empe a u e)
●Biological Sample Cha ac e is ics (e.g., issue ype, diseased s a us,...)
●Hos O ganism Me ada a
Bo h ypes o me ada a ensu es he ep oducibili y and allows o compa ison ac oss di e en
s udies.
Exe cise: Spli in o g oups, hink o a p ojec and collec he echnical me ada a
Di e ence be ween Technical and Biological me ada a
Technical me ada a
Technical me ada a in mic obiology
Is a o m o desc ip i e me ada a ha e e s o he echnical pa o da a gene a ion and p ocessing. This ype o me ada a
ensu es he ep oducibili y o expe imen s and esul s and allows o compa ison ac oss di e en s udies.
Technical me ada a includes (bu is no limi ed o):
1. Sequencing Pla o m In o ma ion
(Type o sequencing echnology, model o
sequence , ead leng h, chemis y, sequencing ki )
2. Sample Collec ion and P ocessing
(When and how he samples we e collec ed, s o ed,
ea men s applied o samples be o e p ocessing)
3. Nucleic Acid Ex ac ion P o ocols
(Me hods ha we e used o sample ex ac ion, ype
o ex ac ion ki o chemicals, nucleic acid
concen a ion, pu i y o ex ac ed ma e ial)
4. Quali y Con ol Measu es
(Me hods o assessing da a quali y and in eg i y o DNA/RNA,
lib a y quali y, sequencing ead quali y)
5. Da a P ocessing and Analysis
(So wa e and algo i hm in o ma ion, e sion numbe ,
pa ame e s se ings o sequence alignmen , assembly,
anno a ion, s a is ical analysis)
6. P ime s Used (i applicable)
(In o ma ion on p obes o oligome s, used in sequencing)
Da a P ocessing and Analysis
Da a P ocessing and Analysis - e sions
Minimal echnical me ada a
h ps://anaconda.o g/ h ps:// s udio.gi hub.io/ en /a icles/
en .h ml
In e ope able ¹⁽ ⁾
¹ Wilkinson, M. D., Dumon ie , M., Aalbe sbe g, I. J. J., Apple on, G., Ax on, M., Baak, A., Blombe g, N., Boi en, J.-W., da Sil a San os, L. B., Bou ne, P. E., &
e al. (2016). The Fai Guiding P inciples o Scien i ic Da a Managemen and S ewa dship. Scien i ic Da a, 3(1). h ps://doi.o g/10.1038/sda a.2016.18
² Ac ion, G. O. D. A. N. (2019). GODAN Ac ion Online Cou se on Open Da a Managemen in Ag icul u e and Nu i ion (Ve sion 1.0). Zenodo.
h ps://doi.o g/10.5281/zenodo.3588148
³ Luiz Ola o Bonino da Sil a San os, Kees Bu ge , Raja am Kaliyape umal, Ma k D. Wilkinson; FAIR Da a Poin : A FAIR-o ien ed app oach o me ada a
publica ion. Da a In elligence 2022; doi: 10.1162/din _a_00160
Wha does i mean “To be In e ope able”:
1. (Me a)da a uses an accessible, b oadly applicable, o mal and sha ed language o
knowledge ep esen a ion (e.g., on ologies, con olled ocabula ies, e c.),
2. (Me a)da a uses ocabula ies ha ollow he FAIR da a p inciples (e.g., using FAIR Da a
Poin ³ ),⁽ ⁾
3. (Me a)da a indica es and includes a quali ied e e ence o (p ima y) o he (me a)da ase s
(when used o newly gene a ed da ase builds upon a p e-exis ing da ase , p ope ly ci ing all
da ase s).
Da ase is in e ope able, when i can be used along o he da ase s, ac oss di e en
sys ems, wi hou special e o om he use ² .⁽ ⁾
Reusable
(Wilkinson e al., 2016)¹
¹ Wilkinson, M. D., Dumon ie , M., Aalbe sbe g, I. J. J., Apple on, G., Ax on, M., Baak, A., Blombe g, N., Boi en, J.-W., da Sil a San os, L. B., Bou ne, P. E., &
e al. (2016). The Fai Guiding P inciples o Scien i ic Da a Managemen and S ewa dship. Scien i ic Da a, 3(1). h ps://doi.o g/10.1038/sda a.2016.18
Wha does i mean “To be Reusable”:
1. (Me a)da a is ichly desc ibed wi h a plu ali y o ele an and accu a e a ibu es
(on ologies/con olled ocabula ies) (e.g., me ada a should desc ibe he con ex unde which
he da a was collec ed o gene a ed),
2. (Me a)da a is published wi h a accessible and clea da a usage license (e.g., CC 0, CC BY
4.0, e c.),
3. (Me a)da a is associa ed wi h de ailed p o enance.
In simples e ms, “How easy is i o euse he da a?”.
Resea ch Da a Li e Cycle
Resea ch Da a Li e Cycle
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RDM - Bene i s and consequences?
¹ Resea ch da a li ecycle. h ps://libguides.n u.edu.sg/ dm/ esea chda ali ecycle
² Bob o , E., Adam, L.-S., Sö ing, S., Jäckel, D., He wig, A., Linds äd , B., Vandendo pe, J., & Shu sko, A. (2021). Wo kshop on Resea ch Da a.
NFDI4Mic obio a - Knowledge Base (h ps://knowledgebase.n di4mic obio a.de/Resea ch-Da a-Managemen /02-
dm.h ml#NTU_LibGuides_RD_li e_cycle)
Bene i s and consequences o poo RDM
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Da a Managemen Plans - DMPs
¹ Assmann, C., Gadelha, L., Ma kus, K., & Vandendo pe, J. (2022). Wo kshop on Resea ch Da a Managemen .
² Bob o , E., Adam, L.-S., Sö ing, S., Jäckel, D., He wig, A., Linds äd , B., Vandendo pe, J., & Shu sko, A. (2021). Wo kshop on Resea ch Da a.
³ B es, E., Rudol , D., Linds äd , B., & Shu sko, A. (2022). Resea ch Da a Managemen in Medical and Biomedical Sciences.
⁴ Engelha d , C., Bie nacka, K., Co ey, A., Co ne , R., Danciu, A., Demchenko, Y., Downes, S., E dmann, C., Ga buglia, F., Ge me , K., Helbig, K., Hells öm,
M., He ne, K., Hibbe , D., Je en, M., Ka imo a, Y., K yge Hansen, K., Kuusniemi, M. E., Le izia, V., … Zhou, B. (2022). D7.4 How o be FAIR wi h you da a.
A eaching and aining handbook o highe educa ion ins i u ions. h ps://doi.o g/10.5281/ZENODO.6674301
⁵ Linds äd , B., Vandendo pe, J., & on de Ropp, S. (2019). Resea ch Da a Managemen .
⁶ Jacob, B., K oehling, M. A., Me zen, D., S aka, J., Linds äd , B., Shu sko, A., & Vandendo pe, J. (2022). Wo kshop on Resea ch Da a.
⁷ Voigh , P., F e icks, S., Linds äd , B., Shu sko, A., & Vandendo pe, J. (2022). Wo kshop on Resea ch Da a.
Bene i s (¹,²,³,⁴,⁵,⁶,⁷):
-Visibili y and clea da a owne ship
-Da a quali y assu ance
-Eligibili y o unding (legal incen i e)
-P e en s da a loss
-Sa es ime, money and esou ces
Consequences:
Da a Managemen Plan(s) - DMPs
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DMPs - Wha do hey include?
Requi ed by DFG (since 2022) and EU Funding P og ams (since 2021).
They ac as epo ing ools o unding agencies, o hold g an ecipien s
accoun able o conduc good and open science.
A companion o p oposal w i ing o sha ing o da a and indings.
DMP - Con en
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How o make a DMP?
-Responsibili ies and obliga ions (who, when, whe e)
-Desc ip ion o he esea ch p ojec (why, how, wha )
-Cos s and esou ces (da a gene a ion, pe sonnel, e c. )
-Desc ip ion o he esea ch da a ( ype, quali y, o ganiza ion and usage)
-Me ada a o be collec ed
-S o age and secu i y (whe e will i be s o ed sho e m, who has access)
-Digi al p ese a ion (long e m s o age/a chi ing, da a p ese a ion)
-Legal aspec s and anonymi y (when dealing wi h sensi i e da a)
¹ Guides o Resea che s. How o ind a us wo hy eposi o y o you da a. h ps://www.openai e.eu/ ind- us wo hy-da a- eposi o y
² England, J., & Tsoukala, V. (2023). Ho izon Eu ope Open Science equi emen s in p ac ice - OpenAIRE webina (Ve sion 2023-11). Zenodo.
h ps://doi.o g/10.5281/zenodo.10125224
Gene a ing a DMP
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Da a o ganiza ion
Resea ch Da a Managemen O ganise - h ps:// dmo ganise .gi hub.io/en/
NFDI4Mic obio aPlan - h ps:// hoelken.gi hub.io/da aplan/ → Exe cise, make you own DMP using his
ool. Wha is i missing.
Example o a good DMP (o is i ?): Molin, E. (2018). Beha e Wo king Da a-Managemen -Plan.
Zenodo. h ps://doi.o g/10.5281/ZENODO.1243717
DMP empla es:
1. Biological & En i onmen al Sciences
a. Ge man Fede a ion o Biological Da a (GFBio): h ps://dmp.g bio.o g/
b. Da aPlan : h ps://n di4plan s.de/da aplan/
2. Heal h Sciences
a. Uni e si y o Minneso a (incl. School o Public Heal h): h ps://www.lib.umn.edu/se ices/da a/dmp-examples
b. Clinical ials
i. Na ional Ins i u es o Heal h (NIH):
h ps://www.nidc .nih.go /si es/de aul / iles/2018-03/clinical-da a-managemen -plan- empla e_0.docx
ii. PAPA-ARTiS:
h ps://ec.eu opa.eu/ esea ch/pa icipan s/documen s/downloadPublic?documen Ids=080166e5b6899b9b&appId=PPGMS
Da a o ganiza ion - 5s me hodology ¹⁽ ⁾
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File naming
1. So : dele e unnecessa y iles.
2. Se in o de : de elop and documen naming con en ions and olde s uc u es.
3. Shine:
a. Comply wi h con en ions.
b. De elop ou ines.
4. S anda dize:
a. Documen ules and esponsibili ies.
b. De elop bes p ac ices and S anda d Ope a ing P ocedu es (SOPs).
5. Sus ain:
a. Regula ly check whe he ules a e ollowed.
b. Implemen imp o emen s i necessa y.
¹ Lang, K., Roman, G., Jessica, R., Anne , S., Nadine, N., & Lehmann, A. (2021). The 5S Me hodology in Resea ch Da a Managemen . Zenodo.
h ps://doi.o g/10.5281/zenodo.4494258
File naming
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File name examples
1. Alphabe ically so able names a e a ou able (e.g. da e YYYY-MM-DD)
2. Ad isable o use up o 32 cha ac e s (e.g. 32Cha ac e sLooksExac lyLikeThis. x )
3. Use name ha is unique o he con en (e.g. 2024-07-09_sample_NODE_R16_A4. n)
4. Don’ use pe iods in he name, only in he ex ension
5. Special cha ac e s (“,|,&,%,$, e c.) and whi espaces (so space o ab) a e con using ( o
compu e s and o he s)
6. Use leading ze os (e.g. om 0001 - 0010 - 0100 - 1000)
¹ Assmann, C., Gadelha, L., Ma kus, K., & Vandendo pe, J. (2022). Wo kshop on Resea ch Da a Managemen .
File name examples
25
Folde s uc u e
1. Good s uc u e ¹⁽ ⁾:
a. YYYY-MM-DD_JV_P ojec ID_Expe imen ID wi h IDs being linked o a able wi h da a
documen a ion such as me ada a
2. Good names ²⁽ ⁾:
a. 2016-01-04_P ojec A_Ex1Tes 1_Smi hE_ 1-0.xlsx
b. 2000_USNM_379221_01. i
c. USNM_379221_01. i
3. Bad names ² :⁽ ⁾
a. Tes da a 2016.xlsx
b. Mee ing no es Jan 17
c. No es E ic. x
d. Final FINAL las e sion.docx
¹ Bob o , E., Adam, L.-S., Sö ing, S., Jäckel, D., He wig, A., Linds äd , B., Vandendo pe, J., & Shu sko, A. (2021). Wo kshop on Resea ch Da a.
² B es, E., Rudol , D., Linds äd , B., & Shu sko, A. (2022). Resea ch Da a Managemen in Medical and Biomedical Sciences.
Da a license - da a and esul s o so wa e
32
Da a and esul s - which license o choose.
By de aul any c ea o o da a, so wa e, w i ing o any o he con en in ol ing a su icien amoun
o c ea i i y is he copy igh owne o ha con en wi hou ha ing o decla e he copy igh
explici ly.
De ining o using a sui able license o published con en usually has he bene i o gi ing all pa ies
legal ce ain y and unde s anding o pe mission o use.
So i is abou whe he and how o he s can use you da a.
In sciences, wo ca ego ies o licenses can applied o ei he so wa e o da a and esul s.
Publishing igu es and a icles in jou nals, usually equi es accep ing he license ag eemen o he
publishe and in ol es ei he a comple e ans e o igh s on you own wo k o picking an open
access jou nal wi h accep able pe missi e licenses.
Da a and Resul s - C ea i e Commons (CC) licenses
33
So wa e licenses.
-CC-BY: C edi mus be gi en o he c ea o .
-CC BY-SA: C edi mus be gi en o he c ea o .
Adap a ions mus be sha ed unde he same e ms.
-CC BY-NC: C edi mus be gi en o he c ea o .
Only noncomme cial uses o he wo k a e pe mi ed.
-CC BY-NC-SA: C edi mus be gi en o he c ea o .
Only noncomme cial uses o he wo k a e pe mi ed.
Adap a ions mus be sha ed unde he same e ms.
-CC BY-ND: C edi mus be gi en o he c ea o .
No de i a i es o adap a ions o he wo k a e pe mi ed.
-CC BY-NC-ND: C edi mus be gi en o he c ea o .
Only noncomme cial uses o he wo k a e pe mi ed.
No de i a i es o adap a ions o he wo k a e pe mi ed.
-CC0: Public domain dedica ion.
So wa e licenses
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How o keep ack o all you (me a)da a.
Exe cise: Go o h ps://opensou ce.o g/licenses
Di ide you sel in “x” g oups o “y” pa icipan s
Find ou wha is he di e ence (i any) be ween:
-MIT
-GPL 2
Think in e ms o :
- euse (comme cial and non-comme cial)
-Pipeline and wo k low implemen a ion
-Adap a ion o wo k (and unde which license he adap ed wo k mus be
published)
Elec onic no ebooks (ELNs)
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Take home message!
So wa e mean o documen expe imen s and esea ch da a.
Some esou ces al eady a ailable (NFDI4Mic obio a in de elopmen )
-SciNo e ELN: A cloud-based ELN wi h lab in en o y, compliance, and eam
managemen ools
-Labgu u ELN: An in ui i e and use - iendly ELN wi h a ocus on lexibili y and
adap abili y
-Lab olde ELN: A cloud-based ELN wi h a cen al posi ion in daily esea ch
wo k lows, enabling easy sha ing o in o ma ion
Take home message
36
Fu he eading
CC-BY 2.0,
h ps://www. lick .com/people/33255628@N00
h ps://en.wikipedia.o g/wiki/
File:Me ada a_is_a_lo e_no e_ o_ he_ u u e_(8071729256).jpg
Resou ces o u he eading - links, explana ions and mo e
NFDI4Mic obio a - Knowledge
Base
NFDI4Mic obio a - Me ada aS anda ds
