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![Page 1: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/1.jpg)
Towards a Data Model
for the
Australian Microbial Resources Information Network
(AMRiN)
Lynette WoodburnAtlas of Living Australia
Version: 0.0317/09/2010
![Page 2: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/2.jpg)
Each slide in this presentation comes with accompanying Notes.
You can’t see them if you display this presentation in ‘Slide Show’ mode.
If you’d like to see the Notes
• view the presentation in ‘Normal’ mode, and • expand the pane below the slide (the Notes pane) to see extra text.
Only then will you have a chance of understanding all the crazy diagrams.
TIP
![Page 3: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/3.jpg)
a standard set of data fields for all micro-organisms
. to support the sharing and integration of data through AMRiN
. to pre-configure BioloMICS
Requirement
Options . choose an existing set
. develop something new
Towards a data model for AMRiN
Recommendation
. surprise!
![Page 4: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/4.jpg)
1. Requirements
2. Options
3. Recommendation
![Page 5: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/5.jpg)
AMRiN
AMRiN community
![Page 6: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/6.jpg)
AMRiN
AMRiN community
![Page 7: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/7.jpg)
AMRiN
AMRiN community
![Page 8: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/8.jpg)
1. Requirements
2. Options
3. Recommendation
- existing
CABRIMCL
![Page 9: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/9.jpg)
Common Access to Biological Resources and Information CABRI
a European organization of partner collections
who contribute data to searchable ‘catalogues’ covering
http://www.cabri.org/
• bacteria & archaea
• fungi & yeasts
• animal & human cell lines
• plant cell lines
• hybridomas
• phages
• plasmids
• plant cell viruses
• genomic libraries
![Page 10: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/10.jpg)
CABRI’s sets of data elements
• 26
• 23
• 29
• 17
• 15
• 33
• 30
• 12
• 7
• bacteria & archaea
• fungi & yeasts
• animal cell lines
• plant cell lines
• hybridomas
• phages
• plasmids
• plant cell viruses
• genomic libraries
elements per set
Original_host_plant
Doubling_time
Lysogenicity
Isolated_from
Morphology
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Common Access to Biological Resources and Information CABRI
For each different kind of biological resource,
CABRI defines nested sets of data elements
Mandatory Recommended Full
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CABRI : bacteria & archaea
Strain_numberOther_collection_numbersRestrictionsOrganism_typeNameInfrasubspecific_namesStatusHistoryConditions_for_growth Form_of_supply
SerovarOther_namesIsolated_fromGeographic_originMutantGenotypeLiterature
Sexual_statePathogenicityEnzyme_productionMetabolite_productionApplicationsCatalogue_entryRemarksPrice_codePlasmids
Mandatory Recommended Full
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CABRI : fungi & yeasts
Strain_numberOther_collection_numbersNameStatusOrganism_typeHistoryRestrictionsForm_of_supplyConditions_for_growth
Misapplied_namesRaceSubstrateGeographic_originLiteratureApplicationsMutantSexual_state
Price_codeRemarksPathogenicityMetabolite_productionEnzyme_productionGenotype
Mandatory Recommended Full
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CABRI : animal & human cell lines
Accession_numberCell_line_nameBrief_descriptionDescriptionDepositorBibliographic_referencesMorphologyCulture_conditionsVirusesPropertiesRelease_conditionsHazard Passage_number
Species_validation
TumorigenicityKaryologyFreezing_mediumSterilityValidation_assaysFurther_bibliographyCommentsStorageDoubling_timeMycoplasmaFingerprintCytogeneticsKaryotypeCommentsResearch_council_depositBIOMED_1
Mandatory Recommended Full
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CABRI’s sets of data elements
• 26
• 23
• 29
• 17
• 15
• 33
• 30
• 12
• 7
• bacteria & archaea
• fungi & yeasts
• animal cell lines
• plant cell lines
• hybridomas
• phages
• plasmids
• plant cell viruses
• genomic libraries
192
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Sharing data about one kind of biological resource is easy
eg. phages
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eg. plasmids
Sharing data about one kind of biological resource is easy
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Sharing data about multiple kinds of biological resources is hard
Other_culture_collection_numbers
Other_collection_numbers
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133 distinct data elements …
for describing several different kinds of biological resources ?
What is the prospect of deriving a common model from CABRI
… distributed across 9 sets
bacte
ria &
arc
haea
fungi & yeasts
animal cell lines
plant cell lines
hybridomas
phag
es plasmids
plant cell viruses
genomic libraries
![Page 20: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/20.jpg)
each of 92 elements is found in only one set
CABRI as a common model ?
only 41 elements are found in more than one set
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CABRI as a common model ?
27 data elements are found in two sets 10 ….. in three 4 ….. in four
No elements are found in more than 4 sets
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Distribution of data elements across CABRI sets
• bacteria & archaea
• fungi & yeasts
• animal cell lines
• hybridomas
• phages
• plant cell lines
• plant cell viruses
• plasmids
• genomic libraries
Count of data elements in one set two three four
6 3 22 7 14 12 9 13 6 11 4 12 2 1 2 2 1 1 1 3 1
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CABRI data element ‘themes’
• bacteria & archaea
• fungi & yeasts
• animal cell lines
• plant cell lines
• hybridomas
• phages
• plasmids
• plant cell viruses
• genomic libraries
ID of item in
collection
Name / classific
ation of it
em
item admin
handling & distributio
n regulatio
ns
care / maintenance
characteristics
literature
….origin
![Page 24: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/24.jpg)
CABRI : comparison of elements across sets
• different names, same meaning (definition)
Accession_number, Strain_number
History, History_of_deposit
Bibliographic_references, Reference_paper, Literature, Reference, Further_bibliography
Restricted_distribution, Release_conditions,Restrictions, Distribution
Morphology, Morphology_and_growth
….
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CABRI : comparison of elements across sets
• same name, different meanings
Brief_description
Type
phages type of elementphage, transposon, minitransposon, IS element, …
plasmids type of elementplasmid, phasmid, cosmid, shuttle vector, transposon, minitransposon, IS element, …
genomic libraries type of libraryPAC, BAC, YAC, PI, cDNA, …
hybridomas listing of species, strain, antibody specificity
animal cell lines listing of species, strain, tissue, tumour, pathology, transformed/transfected
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CABRI : comparison of data element sets
• varying levels of scope
Conditions_for_growth bacteria & archaea
fungi & yeasts
culture medium
atmospheric and light conditions
temperature conditions
additional remarks on cultivation
Medium plasmids, phages
Medium_1 plant cell lines
Light_regime plant cell lines
Light_conditions plant cell lines
Temperature plant cell lines
Humidity plant cell lines
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• 9 sets of data elements (but does not cover algae)
good for sharing information about one kind of organism
• few elements common to several sets
hard to share information about more than one kind of organism • does not lend itself to the derivation of a common set
elements of ‘different names, same meaning’ elements of ‘same name, different meanings’ elements with meanings of varying scope
• has international acceptance / presence (but no longer funded?)
CABRI : fitness for our purpose
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1. Requirements
2. Options
3. Recommendation
- existing
CABRIMCL
![Page 29: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/29.jpg)
Microbiological Common Language
MCL
• a new data exchange standard for microbiological information
Research in Microbiology, 161(6), 439-445
http://www.straininfo.net/projects/mcl
• a pluggable framework, easily extended
• has the same ancestor as CABRI (MINE)
• underpins StrainInfo (www.straininfo.net)
“ a world-wide, virtual catalog integrating the information from BRC [Biological Resource Centres] catalogs with related information”
![Page 30: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/30.jpg)
CABRIMCL
CABRI compared with MCL
partitioned by kind of biological resource partitioned by workflow step
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Sample IsolationCulture
Deposit
Medium Publication
Strain
The abstract model of Microbiological Common Language (MCL)
… follows the logical flow from sampling to subsequent deposits
![Page 32: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/32.jpg)
mcl : Sample
sampleDate
sampleCultureStrainNumber
sampleCollectorsampleCollectorInstitute
comments
sampleDescriptionsampleLocationDescription
sampleLocationCountrysampleLocationPlace
sampleAltsampleLatsampleLong
sampleHabitatEnvoTermsampleHabitat
sampleCulture
Sample
![Page 33: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/33.jpg)
mcl : Culture
Culture
[otherStrainNumbers]
id
cultureLastUpdateDateotherStrainNumberstrainNumber
catalogURL
speciesName
historyisolationDateisolatorisolatorInstituteisolationMethod
typeStrainOfSpeciestypeStrainOf
typeStrainOfGenus
comments
minimalGrowthTemperature[growthTemperature]
optimalGrowthTemperaturemaximalGrowthTemperature
oxygenRelationship
nomenclaturalPublicationpublication
environmentPublicationhistoryPublicationtaxonomicPublication
hasSamplerecommendMedium
![Page 34: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/34.jpg)
some Object Properties
Culture
hasSamplerecommendMedium
nomenclaturalPublicationpublication
environmentPublicationhistoryPublicationtaxonomicPublication
Sample
Medium Publication
![Page 35: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/35.jpg)
mcl : Medium mcl : Publication
Medium
mediumNamemediumNumbermediumURLmediumDescriptioncomments
Publication
dcterms: bibliographicCitationdc: titledc: creatorprism: publicationNameprism: volumeprism: numberprism: startingPageprism: pageRangedcterms: issued
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MCL : fitness for our purpose
• MCL offers a broadly-applicable suite of data elements
. data elements are grouped according to workflow steps, not organism type
. applicable to algae and cyanobacteria
. the Strain concept supports the logical linking of related cultures
• the model is modular and easily extensible
. model cohesion is achieved through Object Properties
. links easily with genomic standards (see StrainInfo)
• born and raised in Europe (StrainInfo), but now going global
. Asian biorepositories network is considering adoption
. we’re invited to contribute to ongoing development
• primarily devised (custom-built) as a data exchange standard
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1. Requirements
2. Options
3. Recommendation
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Recommendation : dip a toe into the water
• MCL, custom-built for describing microbiological data, deserves consideration
Proposal
undertake a pilot, involving a small group of AMRiN participants,
to assess the suitability of MCL for AMRiN’s purpose.
![Page 39: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/39.jpg)
AMRiN
AMRiN community
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AMRiN participants’ input
map local elements to MCL elements
Note:some MCL elements
may not have a local equivalent
identify local elements to be kept ‘private’
identify other local elements to be shared ;
provide English definitionsto enable reconciliation with other participants’ elements
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Pilot assessment
• Coverage?
• What additional common elements exist amongst the set to be shared?
How much orange overlaps purple?
How much purple overlaps purple?
• Other assessment criteria?
![Page 42: Towards a Data Model for the Australian Microbial Resources Information Network (AMRiN) Lynette Woodburn Atlas of Living Australia Version: 0.03 17/09/2010.](https://reader035.fdocuments.in/reader035/viewer/2022081519/56649dea5503460f94ae53be/html5/thumbnails/42.jpg)
Pulling the pieces together
Please consider the foregoing proposal.
Does it seem reasonable to you?
Do you think there’s a better way?