Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language

Adams, Nico; Winter, Jerry; Murray‐Rust, Peter; Rzepa, Henry

doi:10.1021/ci8002123

Cited by 27 publications

(18 citation statements)

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“…Because it is extensible and because computational semantics can be added to some of the elements, it represents a simple functional programming language. This is most developed in PolymerML [40] where a polymer can contain instructions for its own elaboration and the computation is carried out by repeatedly applying polymer extension semantics to the PML representation of the structure.…”

Section: The Philosophy Of CMLmentioning

confidence: 99%

CML: Evolution and design

Murray‐Rust

2011

J Cheminform

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Section: The Philosophy Of CMLmentioning

confidence: 99%

CML: Evolution and design

Murray‐Rust

2011

J Cheminform

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“…CML is currently being investigated by Microsoft Research as a way of introducing semantically rich chemistry features within the Microsoft Office Word package [87]. Adams and Murray-Rust recently reported the development of Polymer Markup Language as a polymer-specific extension to CML [88,89]. Like the Sgroup approach, the language is a fragment-based representation and addresses considerations such as the composition of a given polymer, the structure of a polymer or macromolecule (if known), as well as the records of a computational experiment, physical or other properties of a polymer or macromolecule, experimental metadata, and reaction information.…”

Section: The Semantic Web Of Polymer Datamentioning

confidence: 99%

Polymer Informatics

Adams

2010

Polymer Libraries

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Polymers are arguably the most important set of materials in common use. The increasing adoption of both combinatorial as well as high-throughput approaches, coupled with an increasing amount of interdisciplinarity, has wrought tremendous change in the field of polymer science. Yet the informatics tools required to support and further enhance these changes are almost completely absent. In the first part of the chapter, a critical analysis of the challenges facing modern polymer informatics is provided. It is argued, that most of the problems facing the field today are rooted in the current scholarly communication process and the way in which chemists and polymer scientists handle and publish data. Furthermore, the chapter reviews existing modes of representing and communicating polymer information and discusses the impact, which the emergence of semantic technologies will have on the way in which scientific and polymer data is published and transmitted. In the second part, a review of the use of informatics tools for the prediction of polymer properties and in silico design of polymers is offered.

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“…This means our modifiability requirements mostly focus on how 31 difficult it is to modify either the given format as such (i.e. extend it) or its instance containing data 32 (i.e. transform it): 33 4.…”

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“…86 This means there is no schema for validation 30 based on conventions that could be used with standard XML validation tools. Therefore, users of the 31 format will have to rely on the online CMLLite validator service or they will need to implement their 32 CMLLite-based validator using the available Java library. 86 The later will be probably necessary 33 when validation will need to be performed offline or for many data files that have to be validated 34 often.…”

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Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats

Mokrý

Nic

2015

Preprint

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Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data.While the new format is discussed more in the next article, here we describe our software tools and two stage analysis procedure that supplied the necessary information for the development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, CTfile and XDfile. In addition the following formats were included in the first stage only: CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results:A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. Conclusions:We believe our analysis methodology is potentially highly reusable and could be easily adapted even for domains outside the chemistry area. It is because the methodology and software tools will need only few changes, although analyzed formats and software quality requirements for a format will differ according to the given domain. ABSTRACT BackgroundIn order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software tools and two stage analysis procedure that supplied the necessary information for the development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, CTfile and XDfile. In addition the following formats were included in the first stage only: CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2.

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Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language

Cited by 27 publications

References 29 publications

CML: Evolution and design

CML: Evolution and design

Polymer Informatics

Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats

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