representing scientific databases online andrew markwick jodrell bank centre for astrophysics...
Post on 21-Dec-2015
220 views
TRANSCRIPT
![Page 1: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/1.jpg)
representing scientificdatabases online
andrew markwickjodrell bank centre for astrophysics
university of manchester, [email protected]
![Page 2: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/2.jpg)
motivation
projects
issues with online
![Page 3: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/3.jpg)
![Page 4: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/4.jpg)
![Page 5: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/5.jpg)
![Page 6: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/6.jpg)
![Page 7: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/7.jpg)
designsimple, intuitive
maintain and distributequery by species, reaction
provide reference data and history
technologyPHP/MySQL
HTML, css, javascript
![Page 8: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/8.jpg)
![Page 9: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/9.jpg)
‘sfv2’
w/ JC
![Page 10: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/10.jpg)
designinteractive
save repetition of workcommunity-led and extensible
technologyPHP/MySQL
HTML, css, javascriptFlash, xml
![Page 11: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/11.jpg)
‘spectral line catalogue’on the shoulders of giants
w/ A. Remijan
![Page 12: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/12.jpg)
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
![Page 13: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/13.jpg)
<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’
![Page 14: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/14.jpg)
ALMA Observing Tool
ALMA, Chile, artist’s impression
ALMA – the Atacama Large Millimetre Array
![Page 15: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/15.jpg)
ALMA ‘OT’ – Observing Tool
![Page 16: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/16.jpg)
designALMA–OT – flat & queryable
machine readableone-stop for astronomical spectroscopy
update of (famous) Lovas list
technologyPHP/MySQL, xml
![Page 17: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/17.jpg)
why go ‘online’?
web is world’s #1 information source
= visibility
= accessibility
and not just to your colleagues
![Page 18: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/18.jpg)
use
how is your data(base) used?
usage can drive development
examples
![Page 19: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/19.jpg)
![Page 20: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/20.jpg)
q. What is the most common molecule searched for in udfa?
a. H3+
![Page 21: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/21.jpg)
![Page 22: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/22.jpg)
q. What is the most common molecule searched for that is not in udfa?
a. glycine
![Page 23: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/23.jpg)
![Page 24: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/24.jpg)
q. Spectra from which molecules have been plotted the most times in sfv2?
(i.e. since Feb. 2006)
a. H2O, C2H2, CO2, TiO, HCN, …
![Page 25: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/25.jpg)
![Page 26: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/26.jpg)
use
.. or you can let users drive content directly
e.g. sfv2 requests
usage may influence funding bodies
![Page 27: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/27.jpg)
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
![Page 28: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/28.jpg)
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
![Page 29: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/29.jpg)
just give people what they want
serve data
machine readable
custom format
key / service
![Page 30: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/30.jpg)
two worlds collide
publishing in traditional print journals
funding
online is dynamic- how to reference?
![Page 31: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/31.jpg)
![Page 32: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/32.jpg)
issues
online is lots of work(to do properly)
you can’t just publish and forget
(bizarrely) there is opposition
![Page 33: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/33.jpg)
some ideas worth considering
don’t expose your underlying data model(or at least be v. careful)
limits some abusesprotects against (your own) changes
![Page 34: Representing scientific databases online andrew markwick jodrell bank centre for astrophysics university of manchester, UK andrew.markwick@manchester.ac.uk](https://reader035.vdocuments.us/reader035/viewer/2022062313/56649d635503460f94a462ac/html5/thumbnails/34.jpg)
some ideas worth considering
be aware of technologyyou and your users depend on
keep your own statistics
give people what they want!