Mid e m upda e o you DMP
Ko binian Bösl
Da a managemen coo dina o
Cen e o Digi al Li e & ELIXIR No way
27 No embe 2025
Objec i es
? Ques ions
●How do you backup up you da a?
●How can I make su e da a is unal e ed by s o age o ans e ?
●How can I documen my da a?
! Objec i es
●Check in and upda e you DMP
●Iden i y po en ial gaps in you RDM s a egy
knowledgebase.n di4chem.de/knowledge_base
dmki .elixi -eu ope.o g
Backup
Backup
A oid losing da a!
Use (ins i u ionally) managed s o age wi h
au oma ic backup (and snapsho s?)
OneD i e/Sha epoin @ UiB
A oid: da a solely sa ed o lap ops,
s and-alone HDDs, humb d i es, …
In gene al
3 - 2 -1 ule
3 copies
2 diffe en media
1 off-si e backup
5min o check he backup s a us o you da a
Checksums
Checksum you da a o de ec co up ion du ing s o age o ans e
MD5sum in buil in e e y OS
windows powe shell: $ ce u il -hashfile [filename] MD5
Mac OS/nix: $ md5sum [filename(s)|*] > checksums.md5
$ md5sum -c checksums.md5
Fo secu i y c i ical o legally ele an : sha256
Demo + 5 min o you o checksum one o you da a olde s
Gene: PIK3CA
Sequence iden i ie s:
Figu e 6 om Zhao, S., and Zhang, B. (2015). BMC Genomics 16 licensed unde C ea i e Commons A ibu ion 4.0 In e na ional License
README files
S udy/p ojec le el README
This README ile was gene a ed on [YYYY-MM-DD] by [NAME]
GENERAL INFORMATION
- S udy/p ojec i le:
- Desc ip ion: <p o ide a sho desc ip ion o he s udy/p ojec >
- P inciple In es iga o :
- Link o Da a managemen plan
ORGANIZATION
- Folde s uc u e: simila o olde s uc u e example abo e (below)
- File naming con en ions (wi h examples) <unless you p ojec is big and
you ha e README iles in e e y sub olde wi h his in o ma ion p o ided
he e>
- File o ma s: <P o ide a lis o all ile o ma s p esen in his s udy/p ojec >
Da a le el README
GENERAL INFORMATION
- Da ase i le:
- Desc ip ion: <p o ide desc ip ion o he da ase o igin, s eps used in i s
gene a ion, con en and i s pu pose>
ORGANIZATION
- Folde s uc u e: simila o olde s uc u e example abo e (below)
- File naming con en ions: <p o ide explana ion o he elemen s used,
allowed alues and examples>
- File o ma s: <P o ide a lis o all ile o ma s p esen in his da ase >
[...]
15 min o you o c ea e a README o one o you da a olde s
RDMki -> you ask -> da a
documen a ion
Minimum In o ma ion abou a high- h oughpu
Nucleo ide SeQuencing Expe imen (MINSEQE)
Repo ing s anda ds o e.g. RNA-Seq
In o ma ion ega ding submission on A ayExp ess
h ps://www.ebi.ac.uk/a ayexp ess/submi /o e iew.h ml
MINSEQE en y on FAIRha ing:
h ps:// ai sha ing.o g/bsg-s000174/
h ps://www. ged.o g/p ojec s/minseqe/
Requi ed o deposi ion o sequencing da a on A ayExp ess
MINSEQE
Example
Adminis a i e In o ma ion:
Pe son(s)
O ganisa ions
Publica ions
MINSEQE
Type o me ada a
Adminis a i e In o ma ion:
Pe son(s)
O ganisa ions
Publica ions
Expe imen al Condi ions/Design
P o ocols:
●T ea men
●Sample Collec ion
●G ow h
●Nucleic Acid Ex ac ion
●Lib a y Cons uc ion
●Sequencing P o ocol
Adminis a i e In o ma ion:
Pe son(s)
O ganisa ions
Publica ions
Expe imen al Condi ions/Design
P o ocols:
●T ea men
●Sample Collec ion
●G ow h
●Nucleic Acid Ex ac ion
●Lib a y Cons uc ion
●Sequencing P o ocol
High- h oughpu Sequence Alignmen P o ocol
Da a No maliza ion P o ocol
Adminis a i e In o ma ion:
Pe son(s)
O ganisa ions
Publica ions
Expe imen al Condi ions/Design
P o ocols:
●T ea men
●Sample Collec ion
●G ow h
●Nucleic Acid Ex ac ion
●Lib a y Cons uc ion
●Sequencing P o ocol
High- h oughpu Sequence Alignmen P o ocol
Da a No maliza ion P o ocol
Ensembl ID
Re Seq ID
as q
bam
HTML
cs / s
Adminis a i e In o ma ion:
Pe son(s)
O ganisa ions
Publica ions
Expe imen al Condi ions/Design
P o ocols
High- h oughpu Sequence Alignmen P o ocol
Da a No maliza ion P o ocol
as q
bam
cs / s
Ensembl ID
Re Seq ID
Taxon
Adminis a i e In o ma ion:
Pe son(s)
O ganisa ions
Publica ions
Expe imen al Condi ions/Design
P o ocols
High- h oughpu Sequence Alignmen P o ocol
Da a No maliza ion P o ocol
as q
bam
cs / s
Ensembl ID
Re Seq ID
Taxon
Pa en s in Eu ope
Ac i e p ocess
No p io disclosu e
Apply only in limi ed geog aphical scopes
Fees ( a ying by business size and scope)
Apply o max 20 yea s a e applica ion
h ps://www.digi alli eno way.o g/con e ence/2021/digi al-li e-2021-know-how-wo kshop-ip .h ml
Copy igh in Eu ope
C ea i e p oduc s: so wa e, w i ing, figu es, pho os,...
De ails o so wa e: Di ec i e 2009/24/EC
Applies by de aul
Does no apply o ac s
Economic igh s s. mo al igh s
Au ho li e ime + 70 yea s
Commons:Copy igh ules by e i o y/No way
h ps://lo da a.no/p o/#documen /NL/lo /2018-06-15-40
h ps://eu -lex.eu opa.eu/legal-con en /EN/ALL/?u i=CELEX:32009L0024
h ps://lo da a.no/p o/#documen /NLX2/a ale/a -1992-05-02-1- 17
Example WIPO: Gene ic da a
Raw sequence does no ha e copy igh
P ocessed da a migh ha e
Pa en ing unaffec ed
Special conside a ion ega ding adi ional knowledge (Nagoya p o ocol)
h ps://www.wipo.in /expo /si es/www/ k/en/docs/ip_g _g da aguide in.pd
EU Da abase di ec i e
Defined addi ional (sui gene is) IPR o :
“collec ion[s] o independen wo ks, da a o o he ma e ials [ ha does
no all unde copy igh ] a anged in a sys ema ic o me hodical way and
indi idually accessible by elec onic o o he means”
15 yea s by de aul
h ps://eu -lex.eu opa.eu/eli/di /1996/9/oj
h ps://lo da a.no/p o/#documen /NLX2/a ale/a -1992-05-02-1- 17
Licensing
A licenso may g an a license unde in ellec ual p ope y
laws o au ho ize a use (such as copying so wa e o using
a pa en ed in en ion) o a licensee, spa ing he licensee
om a claim o in ingemen b ough by he licenso .
CC-BY-SA 3.0 License - Wikipedia
Which o hese is de i a i e wo k?
Download some code and use one o he unc ions in you code
Linking o lib a ies (s a ic o dynamic), plug-ins, and d i e s
Clean oom design (you ne e see he code)
Ex ending code you go om somewhe e
Rew i ing code o a diffe en p og amming language
CC-BY 4.0 h ps://code e ine y.gi hub.io/social-coding/licensing/#exe cises-licensing
Which o hese is de i a i e wo k?
✔Download some code and use one o he unc ions in you code
❌Linking o lib a ies (s a ic o dynamic), plug-ins, and d i e s
❌Clean oom design (you ne e see he code)
✔Ex ending code you go om somewhe e
✔Rew i ing code o a diffe en p og amming language
CC-BY 4.0 h ps://code e ine y.gi hub.io/social-coding/licensing/#exe cises-licensing
Why should I licence my esea ch ou pu s?
Why should I licence my esea ch ou pu s?
Legal secu i y o use s (Accessibili y) + Funde equi emen
Why should I licence my esea ch ou pu s?
Legal secu i y o use s (Accessibili y) + Funde equi emen
Inc ease o willingness o euse ou pu s (Reusabili y)
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
CC-BY 4.0 Shaddim; o iginal CC license symbols by h ps://c ea i ecommons.o g/
C ea i e Commons, Na han Ye gle , Alex Robe s. Licensed o he public unde CC BY 3.0 Unpo ed. C ea i e Commons logo
used unde CC T adema k Policy.
C ea i e Commons - Wha is licensed?
Na han Ye gle , Alex Robe s - Who is o be a ibu ed?
Licensed o he public unde CC BY 3.0 Unpo ed - Which license?
CC-BY 4.0 license symbols by h ps://c ea i ecommons.o g/
Challenges
CC-BY 4.0 license symbols by h ps://c ea i ecommons.o g/
Challenges
Mul iple A ibu ions o se e al sou ces (license s acking)
CC-BY 4.0 license symbols by h ps://c ea i ecommons.o g/
Challenges
Mul iple A ibu ions o se e al sou ces (license s acking)
Mul iple incompa ible sou ce licenses
CC-BY 4.0 license symbols by h ps://c ea i ecommons.o g/
Challenges
Mul iple A ibu ions o se e al sou ces (license s acking)
Mul iple incompa ible sou ce licenses
Legal comme cial defini ion (e.g. use by jou nals)
CC-BY 4.0 license symbols by h ps://c ea i ecommons.o g/
Challenges
Mul iple A ibu ions o se e al sou ces (license s acking)
Mul iple incompa ible sou ce licenses
Legal comme cial defini ion (e.g. use by jou nals)
Unin en ional es ic i e
Da abases a e diffe en o simple da a (e.g. EU-copy igh )
Open Da a Commons
Icons CC-BY 4.0
h ps://c ea i ecommons.o g/
h ps://openda acommons.o g
Da abases a e diffe en o simple da a (e.g. EU-copy igh )
Open Da a Commons Public Domain Dedica ion and License
(PDDL)
Open Da a Commons
Icons CC-BY 4.0
h ps://c ea i ecommons.o g/
h ps://openda acommons.o g
Da abases a e diffe en o simple da a (e.g. EU-copy igh )
Open Da a Commons Public Domain Dedica ion and License
(PDDL)
Open Da a Commons A ibu ion License (ODC-By)
Open Da a Commons
Icons CC-BY 4.0
h ps://c ea i ecommons.o g/
h ps://openda acommons.o g
Da abases a e diffe en o simple da a (e.g. EU-copy igh )
Open Da a Commons Public Domain Dedica ion and License
(PDDL)
Open Da a Commons A ibu ion License (ODC-By)
Open Da a Commons Open Da abase License (ODbL)
Open Da a Commons
Icons CC-BY 4.0
h ps://c ea i ecommons.o g/
h ps://openda acommons.o g
Open Sou ce So wa e licenses
MIT license
Apache 2.0
GNU LGPL 3GNU GPL 3
BSD licenses
Icons CC-BY 4.0
h ps://c ea i ecommons.o g/
GNU
AGPL 3
Open Sou ce So wa e licenses
MIT license
Apache 2.0
GNU LGPL 3
GNU
AGPL 3
GNU GPL 3
BSD licenses
Icons CC-BY 4.0
h ps://c ea i ecommons.o g/
h ps://opensou ce.o g/licenses
h ps://choosealicense.com/
Indices & Con olled
ocabula ies
h ps://spdx.o g/licenses/
h ps://opensou ce.o g/licenses
License Lis - maschine eadable IDs
App o ed Licenses - also EC de ini ion
o open sou ce license
on file le el
# SPDX-License-Iden i ie : MIT
MIT
BSD
Icon CC-BY 4.0 h p://so wa e-ca pen y.o g; Image unchanged om h ps://choosealicense.com/
LGPL
MPL
weak
Icon CC-BY 4.0 h p://so wa e-ca pen y.o g; Image unchanged om h ps://choosealicense.com/
Icon CC-BY 4.0 h p://so wa e-ca pen y.o g; Image unchanged om h ps://choosealicense.com/
GPL
AGPL
s ong
Open Sou ce So wa e licenses
CC-BY 4.0
h p://so wa e-ca pen y.o g/
Open Sou ce So wa e licenses
CC-BY 4.0
h p://so wa e-ca pen y.o g/
Open Sou ce So wa e licenses
CC-BY 4.0
h p://so wa e-ca pen y.o g/
Does i hold in cou ?
Yes!
F ee So wa e Founda ion, Inc. . Cisco Sys ems, Inc., 2009
…
Busybox GPL lawsui s 2007-2009
Link o RDMki :
h ps:// dmki .elixi -eu ope.o g/
Digi al Li e 2021: Know-how wo kshop on IPR in digi al bio ech
Da a li e cycle: Sha ing | RDMki
You asks: Licensing | RDMki
EUDAT license choose o da a and so wa e
Choose a License
Licenses & S anda ds | Open Sou ce Ini ia i e
Nex :
h ps://code e ine y.o g/
1. As indica ed he e, all publicly accessible use con ibu ions a e licensed unde C ea i e Commons A ibu ion-Sha eAlike license.
See S acko e flow Te ms o se ice o mo e de ailed in o ma ion.
2. “S anda d” licensing ules apply. So in his case, you would need o emo e he po ion o code you ha e copied om ano he
package be o e being able o elease you so wa e.
3. By de aul you a e no au ho ized o use he con en o a eposi o y when he e is no license. And de i a i e wo k is also no
possible by de aul . O he isks: i may no be clea whe he you can use and dis ibu e (publish) he bugfixed code. Fo he epo
owne s i may no be clea whe he hey can use and dis ibu ed he bugfixed code. Howe e , he au ho s may ha e o go en
o add a license so we sugges you o con ac he au ho s (e.g. make an issue) and ask whe he hey a e willing o add a license.
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esul ing combined so wa e you could use a GPL license. Howe e , e-licensing may no be necessa y.
6. De i a i e wo k would need o be sha ed unde his i al license (e.g. AGPL o GPL), unless he componen s a e only plugins o
lib a ies.
7. I you keep you code o you sel , you may hink you do no need a license. Howe e , emembe ha in mos
companies/uni e si ies, you employe is “owning” you wo k and when you lea e you may no be allowed o “dis ibu e you
code o you u u e sel ”. So he bes is always o add a license!
8. The leas a ac i e licenses o companies wi h p op ie a y so wa e a e licenses whe e you would need o keep an open license
when c ea ing de i a i e wo k. Fo ins ance GPL and and AGPL. The mos a ac i e licenses a e pe missi e licenses whe e hey
can euse, modi y and elicense wi h no condi ions. Fo ins ance MIT, BSD and Apache License.
CC-BY 4.0 h ps://code e ine y.gi hub.io/social-coding/licensing/#exe cises-licensing
Thank you!
Excep whe e o he wise no ed, his wo k is licensed unde a
C ea i e Commons A ibu ion 4.0 In e na ional License
h ps://c ea i ecommons.o g/licenses/by/4.0/
elixi -no way.o g
digi alli eno way.o g
@elixi no way
@Digi al Li
@BoslKo binian
con ac @elixi .no
con ac @digi alli eno way.o g
k[email p o ec ed]
Thank you!
Excep whe e o he wise no ed, his wo k is licensed unde a
C ea i e Commons A ibu ion 4.0 In e na ional License
h ps://c ea i ecommons.o g/licenses/by/4.0/
elixi -no way.o g
digi alli eno way.o g
@elixi no way
@Digi al Li
@BoslKo binian
con ac @elixi .no
con ac @digi alli eno way.o g
k[email p o ec ed]
