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BioXSD 1.1: Enhanced and optimized XML format |
BioXSD has been developed as a universal XML format for the basic types of bioinformatics data that is in particular suitable to be used with Web services [16]. It models common types of data for which a specialized XML Schema (XSD) has not been widely adopted: biomolecular sequences, alignments, sequence feature recor... |
BioXSD 1.0 type AnnotatedSequence can represent annotations of a biomolecular sequence or genome with any types of positioned or non-positioned features, which can be combined in one record. Although the textual serialization of XML is in general more verbose than a tabular format, already the BioXSD 1.0 has included a... |
• not repeating the reference to a sequence in every feature occurrence |
• not repeating the type of feature in every feature occurrence |
• representing multi-segment and multi-point feature occurrences in one feature-occurrence element |
The goal of BioXSD version 1.1 has been to further improve the expressiveness of the BioXSD formats and at the same time focus on optimizations of the data size. The successor of BioXSD 1.0 AnnotatedSequence is BioXSD 1.1 type FeatureRecord. BioXSD 1.1 in general allows more types of sequence positions, distinguishing ... |
Table 5. The allowed content of a BioXSD FeatureRecord |
There is one slight difference in how the GTrack and BioXSD deal with focus of feature records. GTrack defines one operational focus of a concrete dataset. That is the reason why it allows to specify only one type of track locations and only one value column and one edges column at a time, although other values and edg... |
Compared to other generic sequence-feature formats, BioXSD allows defining complex, structured meanings of annotations, as well as complex feature data and metadata, or relations. This would not be conveniently possible in a tabular format and takes advantage of the XML. BioXSD types can freely be combined and included... |
It has, however, been problematic to use XML formats for highly voluminous data such as whole-genome annotations. The textual serialization of XML is more verbose compared to a textual tabular format, and even more compared to a bespoke binary format. Many basic XML-handling tools have high runtime demands for computer... |
Availability of specifications and supporting tools |
The BioXSD 1.1 XML Schema is available at [26]. BioXSD data can be validated by all the main XML validation tools, and consumed and produced programmatically by the bulk of the common XML/XSD-handling libraries. Further information and documentation are available at [27]. |
A complete specification of the GTrack format version 1.0 is attached as Additional file 1 and is also available from the GTrack website [20]. The website also contains supporting tools for the GTrack format, connected to the Genomic HyperBrowser [10,28]. Table 6 contains an overview of all GTrack-related tools availab... |
Table 6. Overview of the webtools available from the GTrack website [20] |
The GTrack format is maintained by Sveinung Gundersen and the BioXSD format is maintained by Matúš Kalaš. Both formats are licensed under the Creative Commons Attribution-NoDerivs 3.0 Unported License [29]. |
The Genomic HyperBrowser [10,28] is built on top of the Galaxy framework [30,31] and provides a large set of statistical investigations tailored for the specific track types of supplied tracks. In order for such analyses to be efficient, the system uses a binary storage scheme internally. In this scheme, the core infor... |
By systematic analysis of informational properties of genomic tracks, we delineated fifteen distinct types of tracks. These track types shed light on the variability of track representations, suggesting that the differences between formats is not only due to preferences and conventions, but also to fundamental differen... |
The identification of core informational properties of tracks, as well as a broad survey of various practicalities concerning existing formats, created a basis for the specification of a new format for genomic data: the GTrack format. By allowing precise interpretation, simple parsing, as well as relatively straightfor... |
BAM: Binary Alignment/Map format; BED: Browser Extensible Data format; ChIP-seq: Chromatin Immunoprecipitation sequencing; EXI: Efficient XML Interchange; F: function; GFF: General Feature Format; GTF: Gene Transfer Format; GVF: Genome Variation Format; GP: genome partition; P: points; LBP: linked base pairs; LF: linke... |
Authors' contributions |
SG, AF, EH and GKS conceived and developed the ideas on track type distinctions. SG, MK, OA and GKS developed the GTrack specification. SG and GKS wrote the main parts of the paper. MK wrote the parts on XML-based track representation and developed BioXSD 1.1. SG and GKS were involved with the development of GTrack-rel... |
Acknowledgements and funding |
Funding was kindly provided by EMBIO, FUGE, UiO, Helse Sør-Øst, and eSysbio (funded by the Research Council of Norway). This work was performed in association with 'Statistics for Innovation', a Centre for Research-Based Innovation funded by the Research Council of Norway. We thank Kai Trengereid for crucial work in de... |
Science 2009, 326(5950):289-293. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL |
2. Generic Feature Format version 3 [] webcite |
4. UCSC genome browser data formats [] webcite |
5. Definition of Gene Transfer Format [] webcite |
6. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K: A standard variation file format for human genome sequences. |
Genome Biol 2010, 11(8):R88. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL |
7. Liu F, Tostesen E, Sundet JK, Jenssen TK, Bock C, Jerstad GI, Thilly WG, Hovig E: The human genomic melting map. |
PLoS Comput Biol 2007., 3(5) OpenURL |
8. Definition of Wiggle Track Format [] webcite |
9. The Sequence Ontology [] webcite |
Genome Biol 2010, 11(12):R121. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL |
13. Web services provided by the Center for Biological Sequence analysis (CBS), Technical University of Denmark [] webcite |
14. UniProt C: The Universal Protein Resource (UniProt) in 2010. |
Nucleic Acids Res 2010, (38 Database Issue):D142-8. OpenURL |
15. Gould CM, Diella F, Via A, Puntervoll P, Gemund C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Trave G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ: ELM: the status of the 2010 eukaryotic linear motif reso... |
Nucleic Acids Res 2010, (38 Database Issue):D167-80. OpenURL |
16. Kalas M, Puntervoll P, Joseph A, Bartaseviciute E, Topfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I: BioXSD: the common data-exchange format for everyday bioinformatics web services. |
Bioinformatics 2010, 26(18):i540-6. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL |
17. Efficient XML Interchange (EXI) Format 1.0 [] webcite |
Bioinformatics 2010, 26(17):2204-2207. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL |
BMC Bioinformatics 2008, 9:523. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL |
20. GTrack [] webcite |
21. BioXSD example 1 [] webcite |
22. BioXSD example 2 [] webcite |
23. BioXSD example 3 [] webcite |
24. BioXSD example 4 [] webcite |
25. BioXSD example 5 [] webcite |
26. Definition of BioXSD version 1.1 [] webcite |
27. [] webcite |
28. The Genomic HyperBrowser [] webcite |
29. Creative Commons Attribution-NoDerivs 3.0 Unported License (CC BY-ND 3.0) [] webcite |
Genome Biol 2010, 11(8):R86. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL |
Curr Protoc Mol Biol 2010, 19:-21. |
Unit 19.10.1 |
32. Oliphant T: Guide to NumPy. Trelgol Trelgol Publishing; 2006. OpenURL |
33. The Python Language Reference [] webcite |
34. GNU General Public License, version 3 [] webcite |
35. Li H: Tabix: fast retrieval of sequence features from generic TAB-delimited files. |
Bioinformatics 2011, 27(5):718-719. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL |
36. Affymetrix CNT File Format [http:/ / SNP_Variation/ Manual/ svs7/ affymetrix_cnt_file_format.html] webcite |
37. VCF (Variant Call Format) version 4.1 [http:/ / wiki/ Analysis/ Variant%20Call%20Format/ vcf-variant-call-format-version-41] webcite |
38. The SAM Format Specification (v1.4-r985) [] webcite |
39. BioHDF [] webcite |
40. FASTA [] webcite |
41. Hoffman MM, Buske OJ, Noble WS: The Genomedata format for storing large-scale functional genomics data. |
Bioinformatics 2010, 26(11):1458-1459. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL |
Re: UX Redesign: Dual Boots / Resize issues / Saving KS |
2011/6/22 Máirín Duffy <duffy fedoraproject org> |
There isn't much we can do for them; they really need to run chkdsk on |
their own. One resource we do have at our disposal is ntfsfix, which is |
a utility that can fix common errors, |
It fixes common errors and then forces windows to run a full check in the next boot. |
but the downside to this is that |
if users press any key while it runs, it'll skip the filesystem check |
operation, rendering the whole process useless. |
That's not a bug we can fix, that's just what windows does... |
So we'll need to lean on |
them and make sure we document well the chkdsk process. Will found this |
following documentation on shrinking partitions in Windows: |
Which is useless, because: |
Windows partitioning tools can't resize the main OS drive (drive C). |
The UI is ugly and not usable, users will have problems with it. |
Resize issues |
screen map. |
There's a complication that resizing introduces. The designers would |
case is not reversible at this time. |
dry-run version. |
A dry-run version of resize would need two components: |
(1) Dry run of the resize to determine how much space we'd get |
(2) A dry run of the RPM transaction to determine how much space we'll |
Well, we can't do rpm transaction dry run in anaconda for network installs before we download everything. |
My idea was, simply adding a new field to comps with auto-generated size requirement for the specific group defaults that will be generated on compose time. (I'm not sure Infra will like this idea though). |
If we want to allow individual package selection, the filed should have the installed size for each package in comps (and be in the package definition, not group definition), not for the whole group. |
There's a complication with upgrades here too, especially during |
As I've mentioned, upgrades doesn't need re-sizing, (and iirc you *can't* change the partition scheme during upgrades). |
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