mzMD: visualization-oriented MS data storage and retrieval
Abstract Motivation Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If...
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| Veröffentlicht in: | Bioinformatics 2022-04, Vol.38 (8), p.2333-2340 |
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| container_title | Bioinformatics |
| container_volume | 38 |
| creator | Yang, Runmin Ma, Jingjing Zhang, Shu Zheng, Yu Wang, Lusheng Zhu, Daming |
| description | Abstract
Motivation
Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high-quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS dataset.
Results
We present mzMD, a new storage format of MS datasets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS datasets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree.
Availability and implementation
The source code is freely available at https://github.com/yrm9837/mzMD-java.
Supplementary information
Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btac098 |
| format | Article |
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Motivation
Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high-quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS dataset.
Results
We present mzMD, a new storage format of MS datasets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS datasets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree.
Availability and implementation
The source code is freely available at https://github.com/yrm9837/mzMD-java.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btac098</identifier><identifier>PMID: 35171986</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Algorithms ; Data Accuracy ; Data Visualization ; Information Storage and Retrieval ; Software</subject><ispartof>Bioinformatics, 2022-04, Vol.38 (8), p.2333-2340</ispartof><rights>The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2022</rights><rights>The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c300t-5f27f63dafe8dbe6b7e3e876632ef284980dca0c91c48cd0a7fab1fc7c5dcb223</cites><orcidid>0000-0002-4344-8791 ; 0000-0001-9395-7247</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,1598,27901,27902</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btac098$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35171986$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Runmin</creatorcontrib><creatorcontrib>Ma, Jingjing</creatorcontrib><creatorcontrib>Zhang, Shu</creatorcontrib><creatorcontrib>Zheng, Yu</creatorcontrib><creatorcontrib>Wang, Lusheng</creatorcontrib><creatorcontrib>Zhu, Daming</creatorcontrib><title>mzMD: visualization-oriented MS data storage and retrieval</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high-quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS dataset.
Results
We present mzMD, a new storage format of MS datasets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS datasets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree.
Availability and implementation
The source code is freely available at https://github.com/yrm9837/mzMD-java.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><subject>Algorithms</subject><subject>Data Accuracy</subject><subject>Data Visualization</subject><subject>Information Storage and Retrieval</subject><subject>Software</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkMtKw0AUhgdRrFZfoWTpJnZumUy6k3qFFhfqOpzMRUaSTJ2ZCPbpjbQK7lydA-f7_wMfQjOCLwmu2Lxx3vXWhw6SU3HeJFC4kgfohHCBc4qL6nDcmShzLjGboNMY3zAuCOf8GE1YQUpSSXGCFt12fb3IPlwcoHXbsc33uQ_O9MnobP2UaUiQxeQDvJoMep0Fk8bzB7Rn6MhCG835fk7Ry-3N8_I-Xz3ePSyvVrliGKe8sLS0gmmwRurGiKY0zMhSCEaNpZJXEmsFWFVEcak0htJCQ6wqVaFVQymbootd7yb498HEVHcuKtO20Bs_xJoKWslCcMlHVOxQFXyMwdh6E1wH4bMmuP72Vv_1Vu-9jcHZ_sfQdEb_xn5EjQDZAX7Y_Lf0C8_4gcM</recordid><startdate>20220412</startdate><enddate>20220412</enddate><creator>Yang, Runmin</creator><creator>Ma, Jingjing</creator><creator>Zhang, Shu</creator><creator>Zheng, Yu</creator><creator>Wang, Lusheng</creator><creator>Zhu, Daming</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4344-8791</orcidid><orcidid>https://orcid.org/0000-0001-9395-7247</orcidid></search><sort><creationdate>20220412</creationdate><title>mzMD: visualization-oriented MS data storage and retrieval</title><author>Yang, Runmin ; Ma, Jingjing ; Zhang, Shu ; Zheng, Yu ; Wang, Lusheng ; Zhu, Daming</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c300t-5f27f63dafe8dbe6b7e3e876632ef284980dca0c91c48cd0a7fab1fc7c5dcb223</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Algorithms</topic><topic>Data Accuracy</topic><topic>Data Visualization</topic><topic>Information Storage and Retrieval</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yang, Runmin</creatorcontrib><creatorcontrib>Ma, Jingjing</creatorcontrib><creatorcontrib>Zhang, Shu</creatorcontrib><creatorcontrib>Zheng, Yu</creatorcontrib><creatorcontrib>Wang, Lusheng</creatorcontrib><creatorcontrib>Zhu, Daming</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Yang, Runmin</au><au>Ma, Jingjing</au><au>Zhang, Shu</au><au>Zheng, Yu</au><au>Wang, Lusheng</au><au>Zhu, Daming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>mzMD: visualization-oriented MS data storage and retrieval</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2022-04-12</date><risdate>2022</risdate><volume>38</volume><issue>8</issue><spage>2333</spage><epage>2340</epage><pages>2333-2340</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high-quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS dataset.
Results
We present mzMD, a new storage format of MS datasets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS datasets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree.
Availability and implementation
The source code is freely available at https://github.com/yrm9837/mzMD-java.
Supplementary information
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>35171986</pmid><doi>10.1093/bioinformatics/btac098</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-4344-8791</orcidid><orcidid>https://orcid.org/0000-0001-9395-7247</orcidid></addata></record> |
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| identifier | ISSN: 1367-4803 |
| ispartof | Bioinformatics, 2022-04, Vol.38 (8), p.2333-2340 |
| issn | 1367-4803 1460-2059 1367-4811 |
| language | eng |
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| source | Oxford Journals Open Access Collection |
| subjects | Algorithms Data Accuracy Data Visualization Information Storage and Retrieval Software |
| title | mzMD: visualization-oriented MS data storage and retrieval |
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