Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK [email protected]

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!

Documents

Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK [email protected]