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representing scientificdatabases online
andrew markwickjodrell bank centre for astrophysics
university of manchester, [email protected]
motivation
projects
issues with online
designsimple, intuitive
maintain and distributequery by species, reaction
provide reference data and history
technologyPHP/MySQL
HTML, css, javascript
‘sfv2’
w/ JC
designinteractive
save repetition of workcommunity-led and extensible
technologyPHP/MySQL
HTML, css, javascriptFlash, xml
‘spectral line catalogue’on the shoulders of giants
w/ A. Remijan
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
<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’
ALMA Observing Tool
ALMA, Chile, artist’s impression
ALMA – the Atacama Large Millimetre Array
ALMA ‘OT’ – Observing Tool
designALMA–OT – flat & queryable
machine readableone-stop for astronomical spectroscopy
update of (famous) Lovas list
technologyPHP/MySQL, xml
why go ‘online’?
web is world’s #1 information source
= visibility
= accessibility
and not just to your colleagues
use
how is your data(base) used?
usage can drive development
examples
q. What is the most common molecule searched for in udfa?
a. H3+
q. What is the most common molecule searched for that is not in udfa?
a. glycine
q. Spectra from which molecules have been plotted the most times in sfv2?
(i.e. since Feb. 2006)
a. H2O, C2H2, CO2, TiO, HCN, …
use
.. or you can let users drive content directly
e.g. sfv2 requests
usage may influence funding bodies
abuseusers:
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
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
just give people what they want
serve data
machine readable
custom format
key / service
two worlds collide
publishing in traditional print journals
funding
online is dynamic- how to reference?
issues
online is lots of work(to do properly)
you can’t just publish and forget
(bizarrely) there is opposition
some ideas worth considering
don’t expose your underlying data model(or at least be v. careful)
limits some abusesprotects against (your own) changes
some ideas worth considering
be aware of technologyyou and your users depend on
keep your own statistics
give people what they want!