Limits...
NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A - Syst. Biol. (2012)

Bottom Line: We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats.The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications.An active, open, community-based development process enables future revision and expansion of NeXML.

View Article: PubMed Central - PubMed

Affiliation: NCB Naturalis, Leiden, The Netherlands. rutger.vos@ncbnaturalis.nl

ABSTRACT
In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.

Show MeSH

Related in: MedlinePlus

NeXML syntax example: TreeBASE OTU annotations. This example shows a single container of OTUs (the otus element) with a single OTU (the otu element) that was submitted to the database with the label Zenodorus cf. orbiculatus. Matching this label to the uBio web service returned a close match with the record for Zenodorus orbiculatus (with the namebank identifier 3546132), which uBio describes as matching the NCBI taxonomy record for Zenodorus cf. orbiculatus d008 (with taxon identifier 393215). The normalized OTU label was defined within the context of TreeBASE study S1787.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3376374&req=5

fig2: NeXML syntax example: TreeBASE OTU annotations. This example shows a single container of OTUs (the otus element) with a single OTU (the otu element) that was submitted to the database with the label Zenodorus cf. orbiculatus. Matching this label to the uBio web service returned a close match with the record for Zenodorus orbiculatus (with the namebank identifier 3546132), which uBio describes as matching the NCBI taxonomy record for Zenodorus cf. orbiculatus d008 (with taxon identifier 393215). The normalized OTU label was defined within the context of TreeBASE study S1787.

Mentions: The TreeBASE archive (Piel et al. 2009) accepts submissions of peer-reviewed studies of phylogenetics in a database that stores comparative data, trees that were inferred from these data, and metadata that records the provenance of these results. The TreeBASE web application attempts to link submitted OTU labels to known taxon names, by submitting the OTU labels to the uBio findIT web service after removing serial numbers or other suffixes. The uBio server then attempts to match the labels (as text strings) against records in its NameBank. The returned matching records may include additional metadata on matches between the record and other resources, such as the NCBI taxonomy. Figure 2 shows an example NeXML document that reports the results of this taxon-matching procedure.Figure 2.


NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A - Syst. Biol. (2012)

NeXML syntax example: TreeBASE OTU annotations. This example shows a single container of OTUs (the otus element) with a single OTU (the otu element) that was submitted to the database with the label Zenodorus cf. orbiculatus. Matching this label to the uBio web service returned a close match with the record for Zenodorus orbiculatus (with the namebank identifier 3546132), which uBio describes as matching the NCBI taxonomy record for Zenodorus cf. orbiculatus d008 (with taxon identifier 393215). The normalized OTU label was defined within the context of TreeBASE study S1787.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376374&req=5

fig2: NeXML syntax example: TreeBASE OTU annotations. This example shows a single container of OTUs (the otus element) with a single OTU (the otu element) that was submitted to the database with the label Zenodorus cf. orbiculatus. Matching this label to the uBio web service returned a close match with the record for Zenodorus orbiculatus (with the namebank identifier 3546132), which uBio describes as matching the NCBI taxonomy record for Zenodorus cf. orbiculatus d008 (with taxon identifier 393215). The normalized OTU label was defined within the context of TreeBASE study S1787.
Mentions: The TreeBASE archive (Piel et al. 2009) accepts submissions of peer-reviewed studies of phylogenetics in a database that stores comparative data, trees that were inferred from these data, and metadata that records the provenance of these results. The TreeBASE web application attempts to link submitted OTU labels to known taxon names, by submitting the OTU labels to the uBio findIT web service after removing serial numbers or other suffixes. The uBio server then attempts to match the labels (as text strings) against records in its NameBank. The returned matching records may include additional metadata on matches between the record and other resources, such as the NCBI taxonomy. Figure 2 shows an example NeXML document that reports the results of this taxon-matching procedure.Figure 2.

Bottom Line: We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats.The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications.An active, open, community-based development process enables future revision and expansion of NeXML.

View Article: PubMed Central - PubMed

Affiliation: NCB Naturalis, Leiden, The Netherlands. rutger.vos@ncbnaturalis.nl

ABSTRACT
In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.

Show MeSH
Related in: MedlinePlus