A names backbone a

graph of taxonomy

Nicky Nicolson RBG Kew

Biodiversity Information Standards (TDWG) annual meeting

Florence Italy -31st October 2013

Three layer model

Name occurrences eg collections

Names

Concepts

Three layer model

Name occurrences

Names eg IPNI amp IF

Concepts

Three layer model

Name occurrences

Names

Concepts monographs

amp regional floras

Names occurrence layer

- Data improvement team ndash 4 people

- Names occurrence database

- Matching and de-duplication processes

- Data matching tool ndash ldquoMatchConfrdquo ndash flexible

configuration of matching logic running

matches as batch jobs

- Not dedicated to names data ndash reusable for

any data-type

- Import export via TCS data standard

Names layer

- Wrapped the existing names systems

- IPNI

- IF (work in progress)

- Data import export via TCS

- Workflows

- submit new names for inclusion

- request modifications to existing names

- Linking to evidence

Linking names to evidence

Literature

bull Digital age name citations linked via DOI

bull Legacy (pre-digital) name citations linked to

BHL (work in progress)

Type specimens

bull Persistent identifier to K specimen records

httpspecimenskeworgherbarium[barcodeID]

Three layer model

Name occurrences eg collections

Names

Concepts

Three layer model

Name occurrences

Names eg IPNI amp IF

Concepts

Three layer model

Name occurrences

Names

Concepts monographs

amp regional floras

Names occurrence layer

- Data improvement team ndash 4 people

- Names occurrence database

- Matching and de-duplication processes

- Data matching tool ndash ldquoMatchConfrdquo ndash flexible

configuration of matching logic running

matches as batch jobs

- Not dedicated to names data ndash reusable for

any data-type

- Import export via TCS data standard

Names layer

- Wrapped the existing names systems

- IPNI

- IF (work in progress)

- Data import export via TCS

- Workflows

- submit new names for inclusion

- request modifications to existing names

- Linking to evidence

Linking names to evidence

Literature

bull Digital age name citations linked via DOI

bull Legacy (pre-digital) name citations linked to

BHL (work in progress)

Type specimens

bull Persistent identifier to K specimen records

httpspecimenskeworgherbarium[barcodeID]

Three layer model

Name occurrences

Names eg IPNI amp IF

Concepts

Three layer model

Name occurrences

Names

Concepts monographs

amp regional floras

Names occurrence layer

- Data improvement team ndash 4 people

- Names occurrence database

- Matching and de-duplication processes

- Data matching tool ndash ldquoMatchConfrdquo ndash flexible

configuration of matching logic running

matches as batch jobs

- Not dedicated to names data ndash reusable for

any data-type

- Import export via TCS data standard

Names layer

- Wrapped the existing names systems

- IPNI

- IF (work in progress)

- Data import export via TCS

- Workflows

- submit new names for inclusion

- request modifications to existing names

- Linking to evidence

Linking names to evidence

Literature

bull Digital age name citations linked via DOI

bull Legacy (pre-digital) name citations linked to

BHL (work in progress)

Type specimens

bull Persistent identifier to K specimen records

httpspecimenskeworgherbarium[barcodeID]

Three layer model

Name occurrences

Names

Concepts monographs

amp regional floras

Names occurrence layer

- Data improvement team ndash 4 people

- Names occurrence database

- Matching and de-duplication processes

- Data matching tool ndash ldquoMatchConfrdquo ndash flexible

configuration of matching logic running

matches as batch jobs

- Not dedicated to names data ndash reusable for

any data-type

- Import export via TCS data standard

Names layer

- Wrapped the existing names systems

- IPNI

- IF (work in progress)

- Data import export via TCS

- Workflows

- submit new names for inclusion

- request modifications to existing names

- Linking to evidence

Linking names to evidence

Literature

bull Digital age name citations linked via DOI

bull Legacy (pre-digital) name citations linked to

BHL (work in progress)

Type specimens

bull Persistent identifier to K specimen records

httpspecimenskeworgherbarium[barcodeID]

Names occurrence layer

- Data improvement team ndash 4 people

- Names occurrence database

- Matching and de-duplication processes

- Data matching tool ndash ldquoMatchConfrdquo ndash flexible

configuration of matching logic running

matches as batch jobs

- Not dedicated to names data ndash reusable for

any data-type

- Import export via TCS data standard

Names layer

- Wrapped the existing names systems

- IPNI

- IF (work in progress)

- Data import export via TCS

- Workflows

- submit new names for inclusion

- request modifications to existing names

- Linking to evidence

Linking names to evidence

Literature

bull Digital age name citations linked via DOI

bull Legacy (pre-digital) name citations linked to

BHL (work in progress)

Type specimens

bull Persistent identifier to K specimen records

httpspecimenskeworgherbarium[barcodeID]

Names layer

- Wrapped the existing names systems

- IPNI

- IF (work in progress)

- Data import export via TCS

- Workflows

- submit new names for inclusion

- request modifications to existing names

- Linking to evidence

Linking names to evidence

Literature

bull Digital age name citations linked via DOI

bull Legacy (pre-digital) name citations linked to

BHL (work in progress)

Type specimens

bull Persistent identifier to K specimen records

httpspecimenskeworgherbarium[barcodeID]

Linking names to evidence

Literature

bull Digital age name citations linked via DOI

bull Legacy (pre-digital) name citations linked to

BHL (work in progress)

Type specimens

bull Persistent identifier to K specimen records

httpspecimenskeworgherbarium[barcodeID]

ldquoCite this specimen asrdquo

httpspecimenskeworgherbarium60152000

Names layer services

Data input

bull Remote submission of names pre-publication

Publishing data out

bull Current awareness feeds of new changed

names

bull Data subsets - suitable for use as the starting

point to build classifications

Structured submission of names

pre-publicationPhytoKeys 26 101ndash112 doi 103897phytokeys265335

Name occurrences

Names IPNI amp IF

Concepts WCS

PhytokeysExternal

classification

system

Taxonomy deals with

relationships between names

ldquoDuboscia macrocarpa was considered as the only

species in the genus by Cheek et al (2004 2011)

Keay (1989) Lebrun amp Stork (1997) and Hawthorne

amp Jongkind (2006) with D viridiflora in synonymy

Lebrun amp Stork (2003) subsequently changed their

view of Duboscia to include two species D

macrocarpa and D polyantha which they had

previously placed in synonymy with D macrocarpa

hellipldquo(continues)

Concepts layer a graph

Concepts layer

taxonomy as a graphbull Names are nodes

bull Typed directed relationships represent

synonymy and taxonomic placement

bull Evidence for taxonomic assertions provided as

references

and again standards based import export using

TCS

Nomenclature name nodes

Taxonomy relations between

nodesDuboscia

Duboscia

macrocarpa

Duboscia

viridiflora

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Structured submission of names

pre-publicationPhytoKeys 26 101ndash112 doi 103897phytokeys265335

Name occurrences

Names IPNI amp IF

Concepts WCS

PhytokeysExternal

classification

system

Taxonomy deals with

relationships between names

ldquoDuboscia macrocarpa was considered as the only

species in the genus by Cheek et al (2004 2011)

Keay (1989) Lebrun amp Stork (1997) and Hawthorne

amp Jongkind (2006) with D viridiflora in synonymy

Lebrun amp Stork (2003) subsequently changed their

view of Duboscia to include two species D

macrocarpa and D polyantha which they had

previously placed in synonymy with D macrocarpa

hellipldquo(continues)

Concepts layer a graph

Concepts layer

taxonomy as a graphbull Names are nodes

bull Typed directed relationships represent

synonymy and taxonomic placement

bull Evidence for taxonomic assertions provided as

references

and again standards based import export using

TCS

Nomenclature name nodes

Taxonomy relations between

nodesDuboscia

Duboscia

macrocarpa

Duboscia

viridiflora

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Name occurrences

Names IPNI amp IF

Concepts WCS

PhytokeysExternal

classification

system

Taxonomy deals with

relationships between names

ldquoDuboscia macrocarpa was considered as the only

species in the genus by Cheek et al (2004 2011)

Keay (1989) Lebrun amp Stork (1997) and Hawthorne

amp Jongkind (2006) with D viridiflora in synonymy

Lebrun amp Stork (2003) subsequently changed their

view of Duboscia to include two species D

macrocarpa and D polyantha which they had

previously placed in synonymy with D macrocarpa

hellipldquo(continues)

Concepts layer a graph

Concepts layer

taxonomy as a graphbull Names are nodes

bull Typed directed relationships represent

synonymy and taxonomic placement

bull Evidence for taxonomic assertions provided as

references

and again standards based import export using

TCS

Nomenclature name nodes

Taxonomy relations between

nodesDuboscia

Duboscia

macrocarpa

Duboscia

viridiflora

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Taxonomy deals with

relationships between names

ldquoDuboscia macrocarpa was considered as the only

species in the genus by Cheek et al (2004 2011)

Keay (1989) Lebrun amp Stork (1997) and Hawthorne

amp Jongkind (2006) with D viridiflora in synonymy

Lebrun amp Stork (2003) subsequently changed their

view of Duboscia to include two species D

macrocarpa and D polyantha which they had

previously placed in synonymy with D macrocarpa

hellipldquo(continues)

Concepts layer a graph

Concepts layer

taxonomy as a graphbull Names are nodes

bull Typed directed relationships represent

synonymy and taxonomic placement

bull Evidence for taxonomic assertions provided as

references

and again standards based import export using

TCS

Nomenclature name nodes

Taxonomy relations between

nodesDuboscia

Duboscia

macrocarpa

Duboscia

viridiflora

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Concepts layer a graph

Concepts layer

taxonomy as a graphbull Names are nodes

bull Typed directed relationships represent

synonymy and taxonomic placement

bull Evidence for taxonomic assertions provided as

references

and again standards based import export using

TCS

Nomenclature name nodes

Taxonomy relations between

nodesDuboscia

Duboscia

macrocarpa

Duboscia

viridiflora

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Concepts layer

taxonomy as a graphbull Names are nodes

bull Typed directed relationships represent

synonymy and taxonomic placement

bull Evidence for taxonomic assertions provided as

references

and again standards based import export using

TCS

Nomenclature name nodes

Taxonomy relations between

nodesDuboscia

Duboscia

macrocarpa

Duboscia

viridiflora

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Nomenclature name nodes

Taxonomy relations between

nodesDuboscia

Duboscia

macrocarpa

Duboscia

viridiflora

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Hold data on relationships to

provide evidence

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

AccordingTo WCS

Year2001

Ref doi101234567899

RefType Monographic

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Reuse the nodes to support

different taxonomic opinions

Duboscia

Duboscia

macrocarpa

Duboscia

viridiflora

AccordingTo FWTA

Year1971

Ref doi106789123000

RefType Floristic

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Persistent identification of

concepts

We can re-create a sub-graph representing a concept at

a particular point in time using

1 Name ID

2 Classification

3 State

Users can link to a stable state of a concept

We can provide a feed of what has changed since

Thanks

nnicolsonkeworg

nickynicolson

Thanks

nnicolsonkeworg

nickynicolson