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representing scientific databases online andrew markwick jodrell bank centre for astrophysics

representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk. motivation projects issues with online. design simple, intuitive maintain and distribute query by species, reaction

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representing scientific databases online andrew markwick jodrell bank centre for astrophysics

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  1. representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk

  2. motivation projects issues with online

  3. design simple, intuitive maintain and distribute query by species, reaction provide reference data and history technology PHP/MySQL HTML, css, javascript

  4. ‘sfv2’ w/ JC

  5. design interactive save repetition of work community-led and extensible technology PHP/MySQL HTML, css, javascript Flash, xml

  6. ‘spectral line catalogue’ on the shoulders of giants w/ A. Remijan

  7. curl http://find.nrao.edu/splata-slap/slap?REQUEST=queryData&WAVELENGTH=0.00260075/0.00260080 <?xml version="1.0" encoding="UTF-8"?> <VOTABLE xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance xsi:noNamespaceSchemaLocation=” xmlns:http://www.ivoa.net/xml/VOTable/VOTable-1.1.xsd” version="1.1"> <RESOURCE type="results"> <DESCRIPTION>Splatalogue SLAP Service</DESCRIPTION> <INFO name="QUERY_STATUS" value="OK"/> <INFO name="dbName" value="splat"/> <INFO name="tableName"/> <INFO name="REQUEST" value="queryData"/> <INFO name="WAVELENGTH" value="0.00260075/0.00260080"/> <INFO name="ServiceEngine" value="slap: SLAP version 1.0 DALServer version 0.3"/> <INFO name="TableRows" value="21"/> <TABLE> <FIELD ID="title" name="title" datatype="char" ucd="em.line" utype="ssldm:Line.title" arraysize="*"> <DESCRIPTION>small description identifying the line</DESCRIPTION> </FIELD> <FIELD ID="catname" name="catalog name" datatype="char" ucd="meta.id;meta.table" arraysize="*"> <DESCRIPTION>the name of the line catalog this entry was drawn from</DESCRIPTION> </FIELD> <FIELD ID="wavelength" name="wavelength" datatype="double" ucd="em.wl" utype="ssldm:Line.wavelength.value" unit="m"> <DESCRIPTION>the wavelength in the vacuum of the transition originating the line</DESCRIPTION> </FIELD> <FIELD ID="frequency" name="frequency" datatype="double" ucd="em.freq;spect.line" unit="MHz"> <DESCRIPTION>The molecular formula which may include notation of the common quantum state of the transition</DESCRIPTION> </FIELD> <FIELD ID="molformula" name="molecular formula" datatype="char" ucd="phys.atmol.element" arraysize="*"> <DESCRIPTION>The molecular formula which may include notation of the common quantum state of the transition</DESCRIPTION> </FIELD> <FIELD ID="moltype" name="molecule type" datatype="int"> <DESCRIPTION>The type of molecular given as an integer identifier</DESCRIPTION> </FIELD> <FIELD ID="recommended" name="frequency recommended" datatype="int"> <DESCRIPTION>an integer flag indicating whether this record provides the recommended frequency for this line.</DESCRIPTION> </FIELD> <FIELD ID="QNs" name="quantum numbers" datatype="char" ucd="phys.atmol.transition;spect.line" arraysize="*"> <DESCRIPTION>The initial and final quantum number states that produces this line</DESCRIPTION> </FIELD> <GROUP ID="Line" name="Line" utype="ssldm:Line"> <DESCRIPTION>a description of the spectral line</DESCRIPTION> <FIELDref ref="title"/> <FIELDref ref="wavelength"/> </GROUP> online is more than the web TM

  8. <DATA> <TABLEDATA> <TR><TD>JPL: CH2OHCOCH2OH v29=1 65(10,55)-65( 9,56)</TD><TD>JPL</TD><TD>0.0026007993198247656</TD><TD>115269.3542</TD><TD>CH2OHCOCH2OH v29=1</TD><TD>0</TD><TD></TD><TD>65(10,55)-65( 9,56)</TD></TR> <TR><TD>JPL: NH2CO2CH3 v=1 9( 4, 6)- 8( 3, 6) E</TD><TD>JPL</TD><TD>0.00260079801795189</TD><TD>115269.4119</TD><TD>NH2CO2CH3 v=1</TD><TD>0</TD><TD></TD><TD> 9( 4, 6)- 8( 3, 6) E</TD></TR> <TR><TD>JPL: NH2CO2CH3 v=1 9( 4, 6)- 8( 3, 6) E</TD><TD>JPL</TD><TD>0.002600797618590801</TD><TD>115269.4296</TD><TD>NH2CO2CH3 v=1</TD><TD>0</TD><TD></TD><TD> 9( 4, 6)- 8( 3, 6) E</TD></TR> <TR><TD>JPL: (CH3)2CO v=0 54(33,21)-54(32,22) EE</TD><TD>JPL</TD><TD>0.0026007950374124845</TD><TD>115269.544</TD><TD>(CH3)2CO v=0</TD><TD>1</TD><TD>1</TD><TD>54(33,21)-54(32,22) EE</TD></TR> <TR><TD>JPL: cis-CH2OHCHO v=1 14( 2,13)-14( 1,14)</TD><TD>JPL</TD><TD>0.0026007933722844356</TD><TD>115269.6178</TD><TD>cis-CH2OHCHO v=1</TD><TD>0</TD><TD></TD><TD>14( 2,13)-14( 1,14)</TD></TR> <TR><TD>JPL: C3H8 N/A</TD><TD>JPL</TD><TD>0.0026007911904735396</TD><TD>115269.7145</TD><TD>C3H8</TD><TD>0</TD><TD></TD><TD>N/A</TD></TR> <TR><TD>JPL: C3H8 N/A</TD><TD>JPL</TD><TD>0.0026007911882172737</TD><TD>115269.7146</TD><TD>C3H8</TD><TD>0</TD><TD></TD><TD>N/A</TD></TR> <TR><TD>JPL: NH2CO2CH3 v=1 23(20, 3)-24(19, 5) E</TD><TD>JPL</TD><TD>0.002600789356130706</TD><TD>115269.7958</TD><TD>NH2CO2CH3 v=1</TD><TD>0</TD><TD></TD><TD>23(20, 3)-24(19, 5) E</TD></TR> <TR><TD>JPL: C3H8 N/A</TD><TD>JPL</TD><TD>0.0026007859830224104</TD><TD>115269.9453</TD><TD>C3H8</TD><TD>0</TD><TD></TD><TD>N/A</TD></TR> <TR><TD>JPL: NH2CO2CH3 v=1 23(20, 3)-24(19, 5) E</TD><TD>JPL</TD><TD>0.0026007822579477637</TD><TD>115270.1104</TD><TD>NH2CO2CH3 v=1</TD><TD>0</TD><TD></TD><TD>23(20, 3)-24(19, 5) E</TD></TR> <TR><TD>JPL: NH2CO2CH3 v=1 23(20, 3)-24(19, 5) E</TD><TD>JPL</TD><TD>0.002600781919510257</TD><TD>115270.1254</TD><TD>NH2CO2CH3 v=1</TD><TD>0</TD><TD></TD><TD>23(20, 3)-24(19, 5) E</TD></TR> <TR><TD>JPL: C3H8 N/A</TD><TD>JPL</TD><TD>0.002600780777848383</TD><TD>115270.176</TD><TD>C3H8</TD><TD>0</TD><TD></TD><TD>N/A</TD></TR> <TR><TD>JPL: C2H5OOCH-trans 21( 9,12)-20( 9,11)</TD><TD>JPL</TD><TD>0.0026007731630344477</TD><TD>115270.5135</TD><TD>C2H5OOCH-trans</TD><TD>0</TD><TD></TD><TD>21( 9,12)-20( 9,11)</TD></TR> <TR><TD>JPL: C2H5OOCH-trans 21( 9,13)-20( 9,12)</TD><TD>JPL</TD><TD>0.0026007731630344477</TD><TD>115270.5135</TD><TD>C2H5OOCH-trans</TD><TD>0</TD><TD></TD><TD>21( 9,13)-20( 9,12)</TD></TR> <TR><TD>JPL: NH2CH2CH2OH v26=1 18( 4,14)-17( 5,13)</TD><TD>JPL</TD><TD>0.002600759664053141</TD><TD>115271.1118</TD><TD>NH2CH2CH2OH v26=1</TD><TD>0</TD><TD></TD><TD>18( 4,14)-17( 5,13)</TD></TR> <TR><TD>CDMS: CO v=0 1-0</TD><TD>CDMS</TD><TD>0.0026007576334647012</TD><TD>115271.2018</TD><TD>CO v=0</TD><TD>1</TD><TD></TD><TD>1-0</TD></TR> <TR><TD>JPL: CO v=0 1-0</TD><TD>JPL</TD><TD>0.0026007576334647012</TD><TD>115271.2018</TD><TD>CO v=0</TD><TD>1</TD><TD></TD><TD>1-0</TD></TR> <TR><TD>Lovas/NIST: CO v=0 1-0</TD><TD>Lovas/NIST</TD><TD>0.002600757628952286</TD><TD>115271.202</TD><TD>CO v=0</TD><TD>1</TD><TD></TD><TD>1-0</TD></TR> <TR><TD>SLAIM: CO v=0 1- 0</TD><TD>SLAIM</TD><TD>0.002600757628952286</TD><TD>115271.202</TD><TD>CO v=0</TD><TD>1</TD><TD>1</TD><TD> 1- 0</TD></TR> <TR><TD>CDMS: FeCO N=14-13, J=13-12</TD><TD>CDMS</TD><TD>0.0026007539084712634</TD><TD>115271.3669</TD><TD>FeCO</TD><TD>0</TD><TD></TD><TD>N=14-13, J=13-12</TD></TR> <TR><TD>CDMS: CH3CHNH2COOH - I 29(11,18)-29( 8,21)</TD><TD>CDMS</TD><TD>0.002600753536198126</TD><TD>115271.3834</TD><TD>CH3CHNH2COOH - I</TD><TD>0</TD><TD></TD><TD>29(11,18)-29( 8,21)</TD></TR> </TABLEDATA> </DATA> </TABLE> </RESOURCE> </VOTABLE> VOTABLE as in ‘Virtual Observatory’

  9. ALMA Observing Tool ALMA – the Atacama Large Millimetre Array ALMA, Chile, artist’s impression

  10. ALMA ‘OT’ – Observing Tool

  11. design ALMA–OT – flat & queryable machine readable one-stop for astronomical spectroscopy update of (famous) Lovas list technology PHP/MySQL, xml

  12. why go ‘online’? web is world’s #1 information source = visibility = accessibility and not just to your colleagues

  13. use how is your data(base) used? usage can drive development examples

  14. q. What is the most common molecule searched for in udfa? a. H3+

  15. q. What is the most common molecule searched for that is not in udfa? a. glycine

  16. q. Spectra from which molecules have been plotted the most times in sfv2? (i.e. since Feb. 2006) a. H2O, C2H2, CO2, TiO, HCN, …

  17. use .. or you can let users drive content directly e.g. sfv2 requests usage may influence funding bodies

  18. abuse users: will find errors and inconsistencies (but this is good) will misuse data and your service (so don’t expose yourself too much, and do have lots of validation) users rarely read documentation

  19. idealism vs. practicality idealism where are you? practicality ‘standards’ beautiful, detailed, generic, unambiguous data model vs. what works for you and/or your user? [heresy] is xml best? just give people what they want

  20. just give people what they want serve data machine readable custom format key / service

  21. two worlds collide publishing in traditional print journals funding online is dynamic - how to reference?

  22. issues online is lots of work (to do properly) you can’t just publish and forget (bizarrely) there is opposition

  23. some ideas worth considering don’t expose your underlying data model (or at least be v. careful) limits some abuses protects against (your own) changes

  24. some ideas worth considering be aware of technology you and your users depend on keep your own statistics give people what they want!

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