CCL: Computational Chemistry Ontology
- From: <m.dominic.ryan^gmail.com>
- Subject: CCL: Computational Chemistry Ontology
- Date: Mon, 11 Nov 2024 09:12:33 -0500
I think the pointers previously cited give a good overview of the problem
of ontology in computational chemistry. That term is too broad for usefully
defining an ontology. You really need to identify the problem space you are
working in such as cheminformatics based on data extracted from ELNs, or assay
definitions and types that you might troll through in pulling data from PubChem
etc. Or, the various tools used in QM applications with terms ranging from basis
sets to density functionals etc.
But on the philosophy side I’ll quibble a bit on what was said.
The quantization of physical phenomena is the ‘law of nature’. It
is captured effectively in Schroedinger’s equation due to that
mathematical formalism. Quantum mechanics is an approximation to solutions of
Schoedinger’s equation. As computational power has increased over the
decades we are increasingly able to approach useful problem spaces. That is
often through the combination of methods of varying treatment of electron
correlation and dispersion. The severe scaling of problems means that we still
can only approximate fine details of larger problems.
The question usually comes down to what level of detail matters to your problem.
Do you want to get some idea of how a protein can move around your ligand?
Various approaches to molecular dynamics will do very nicely. But, you could add
a more sophisticated handling of water through additional DFT evaluation of each
step and add correction factor forces to the MD. Are you trying to model light
harvesting proteins and account for energetics of photon to electron shift?
That’s going to need more.
DFT, coupled cluster methods, or pure molecular mechanics are simply empirical
formalisms that are useful in the right setting.
We can extend this to QSAR in a dramatic example. If you compile enough examples
of a problem space and develop a mathematical model that represents that space
with high confidence, have you identified a ‘law of nature’? The
recent Nobel Prize on protein folding is just that. All these ‘AI’
methods are well fitted models, often simply with very deep (many layered)
neural nets to model the phenomena. Even in this space though, there are still
exceptions.
So, how much ‘truth’ do you want with your ontology?
Dominic Ryan
> From: owner-chemistry+m.dominic.ryan==gmail.com+*+ccl.net
<owner-chemistry+m.dominic.ryan==gmail.com+*+ccl.net> On Behalf Of David
Young zqmuser]![gmail.com
Sent: Sunday, November 10, 2024 8:18 AM
To: Ryan, M Dominic <m.dominic.ryan+*+gmail.com>
Subject: CCL: Computational Chemistry Ontology
Darren,
Quantum chemistry is an application of quantum mechanics, which is generally
accepted as a law of nature, so follow the ontology for laws of nature.
Molecular mechanics & dynamics are based on other laws of nature (i.e.
Hook's Law of Elasticity), which are not strictly the correct formulation but
have been validated as giving results that match to experiment to a reasonable
accuracy within a certain region (near equilibrium geometry). The constants in
these equations are fitted to reproduce experimental data.
Some of the cheminformatics methods, like QSAR and QSPR, are completely
empirical. Although they are not derived from any law of nature, they can give
results accurate enough to be useful for certain research needs.
Dave Young (he, him, Dr., scientist, fencer, author)
The wise person tries to find the truth.
The foolish person believes whoever tells them what they want to hear.
On Sun, Nov 10, 2024 at 6:40 AM Darren Rhodes darren.rhodes!^!gmail.com
<http://gmail.com>;
<owner-chemistry[a]ccl.net <mailto:owner-chemistry[a]ccl.net> > wrote:
Sent to CCL by: "Darren Rhodes" [darren.rhodes]|[gmail.com <http://gmail.com>; ]
Hi All
Can you point me in the direction of an appropriate ontology for use in
computational chemistry?
all the best
Darren.
darren.rhodes.:.REMOVEgmail.com
-= This is automatically added to each message by the mailing script =-<br
E-mail to subscribers: CHEMISTRY[a]ccl.net <mailto:CHEMISTRY[a]ccl.net> or use:E-mail to administrators:
CHEMISTRY-REQUEST[a]ccl.net <mailto:CHEMISTRY-REQUEST[a]ccl.net> or use<brJob: http://www.ccl.net/jobs
<br------=_NextPart_000_0113_01DB3419.D85334C0
Content-Type: text/html;
charset="utf-8"
Content-Transfer-Encoding: quoted-printable
<html xmlns:v="urn:schemas-microsoft-com:vml"
xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml";
xmlns="http://www.w3.org/TR/REC-html40"><head><meta
http-equiv=Content-Type content="text/html; charset=utf-8"><meta
name=Generator content="Microsoft Word 15 (filtered
medium)"><style><!--
/* Font Definitions */
+*+font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
+*+font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
+*+font-face
{font-family:"Palatino Linotype";
panose-1:2 4 5 2 5 5 5 3 3 4;}
+*+font-face
{font-family:Aptos;}
+*+font-face
{font-family:Georgia;
panose-1:2 4 5 2 5 4 5 2 3 3;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:12.0pt;
font-family:"Aptos",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Palatino Linotype",serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
+*+page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body
lang=EN-US link=blue vlink=purple style='word-wrap:break-word'><div
class=WordSection1><p class=MsoNormal><span
style='font-size:11.0pt;font-family:"Palatino Linotype",serif'>I
think the pointers previously cited give a good overview of the problem of
ontology in computational chemistry. That term is too broad for usefully
defining an ontology. You really need to identify the problem space you are
working in such as cheminformatics based on data extracted from ELNs, or assay
definitions and types that you might troll through in pulling data from PubChem
etc. Or, the various tools used in QM applications with terms ranging from basis
sets to density functionals
etc.<o:p></o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'>But on the philosophy side I’ll quibble a bit on
what was said. <o:p></o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'>The quantization of physical phenomena is the
‘law of nature’. It is captured effectively in
Schroedinger’s equation due to that mathematical formalism. Quantum
mechanics is an approximation to solutions of Schoedinger’s equation. As
computational power has increased over the decades we are increasingly able to
approach useful problem spaces. That is often through the combination of methods
of varying treatment of electron correlation and dispersion. The severe scaling
of problems means that we still can only approximate fine details of larger
problems.<o:p></o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'>The question usually comes down to what level of detail
matters to your problem. Do you want to get some idea of how a protein can move
around your ligand? Various approaches to molecular dynamics will do very
nicely. But, you could add a more sophisticated handling of water through
additional DFT evaluation of each step and add correction factor forces to the
MD. Are you trying to model light harvesting proteins and account for energetics
of photon to electron shift? That’s going to need more.
<o:p></o:p></span></p><p class=MsoNormal><span
style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'>DFT, coupled cluster methods, or pure molecular
mechanics are simply empirical formalisms that are useful in the right setting.
<o:p></o:p></span></p><p class=MsoNormal><span
style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'>We can extend this to QSAR in a dramatic example. If
you compile enough examples of a problem space and develop a mathematical model
that represents that space with high confidence, have you identified a
‘law of nature’? The recent Nobel Prize on protein folding is just
that. All these ‘AI’ methods are well fitted models, often simply
with very deep (many layered) neural nets to model the phenomena. Even in this
space though, there are still
exceptions.<o:p></o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'>So, how much ‘truth’ do you want with
your ontology? <o:p></o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'>Dominic
Ryan<o:p></o:p></span></p><p
class=MsoNormal><span style='font-size:11.0pt;font-family:"Palatino
Linotype",serif'><o:p> </o:p></span></p><div
style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in
0in'><p class=MsoNormal style='margin-left:.5in'><b><span
style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span
style='font-size:11.0pt;font-family:"Calibri",sans-serif'>
owner-chemistry+m.dominic.ryan==gmail.com+*+ccl.net
<owner-chemistry+m.dominic.ryan==gmail.com+*+ccl.net> <b>On
Behalf Of </b>David Young
zqmuser]![gmail.com<br><b>Sent:</b> Sunday, November 10, 2024
8:18 AM<br><b>To:</b> Ryan, M Dominic
<m.dominic.ryan+*+gmail.com><br><b>Subject:</b>
CCL: Computational Chemistry
Ontology<o:p></o:p></span></p></div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p><div><div><p
class=MsoNormal
style='margin-left:.5in'>Darren,<o:p></o:p></p></div><div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p></div><div><p
class=MsoNormal style='margin-left:.5in'>Quantum chemistry is an application
of quantum mechanics, which is generally accepted as a law of nature, so follow
the ontology for laws of
nature.<o:p></o:p></p></div><div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p></div><div><p
class=MsoNormal style='margin-left:.5in'>Molecular mechanics &
dynamics are based on other laws of nature (i.e. Hook's Law of Elasticity),
which are not strictly the correct formulation but have been validated as giving
results that match to experiment to a reasonable accuracy within a certain
region (near equilibrium geometry). The constants in these equations
are fitted to reproduce experimental
data.<o:p></o:p></p></div><div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p></div><div><p
class=MsoNormal style='margin-left:.5in'>Some of the cheminformatics methods,
like QSAR and QSPR, are completely empirical. Although they are not derived from
any law of nature, they can give results accurate enough to be useful for
certain research
needs.<o:p></o:p></p></div><div><p
class=MsoNormal style='margin-left:.5in'><br
clear=all><o:p></o:p></p></div><div><div><div><div><p
class=MsoNormal style='margin-left:.5in'><b><span
style='font-size:13.5pt;font-family:"Georgia",serif;color:blue;background:white'>Dave
Young (he, him, Dr., scientist, fencer,
author)</span></b><o:p></o:p></p><div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p></div><div><div><p
class=MsoNormal style='margin-left:.5in'><span
style='color:#741B47'>The wise person tries to find the
truth.</span><o:p></o:p></p></div><div><p
class=MsoNormal style='margin-left:.5in'><span
style='color:#741B47'>The foolish person believes whoever tells them what
they want to
hear.</span><o:p></o:p></p></div></div><div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p></div></div></div></div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p></div><p
class=MsoNormal
style='margin-left:.5in'><o:p> </o:p></p><div><div><p
class=MsoNormal style='margin-left:.5in'>On Sun, Nov 10, 2024 at 6:40<span
style='font-family:"Arial",sans-serif'> </span>AM
Darren Rhodes darren.rhodes!^!<a href="http://gmail.com";>gmail.com</a> <<a href="mailto:owner-chemistry[a]ccl.net";>owner-chemistry[a]ccl.net</a>>
wrote:<o:p></o:p></p></div><blockquote
style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in
6.0pt;margin-left:4.8pt;margin-right:0in'><p class=MsoNormal
style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in'><br>Sent
to CCL by: "Darren Rhodes" [darren.rhodes]|[<a
href="http://gmail.com";
target="_blank">gmail.com</a>]<br>Hi
All<br><br>Can you point me in the direction of an appropriate
ontology for use in <br>computational chemistry?<br><br>all
the
best<br><br>Darren.<br>darren.rhodes.:.REMOVEgmail.com<br><br><br><br>-=
This is automatically added to each message by the mailing script
=-<br<br><br><br>E-mail to subscribers: <a
href="mailto:CHEMISTRY[a]ccl.net";
target="_blank">CHEMISTRY[a]ccl.net</a> or
use:<br> <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message";
target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>E-mail
to administrators: <a href="mailto:CHEMISTRY-REQUEST[a]ccl.net";
target="_blank">CHEMISTRY-REQUEST[a]ccl.net</a> or
use<br> <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message";
target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br<br>
<a href="http://www.ccl.net/chemistry/sub_unsub.shtml";
target="_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br><br>Before
posting, check wait time at: <a href="http://www.ccl.net";
target="_blank">http://www.ccl.net</a><br><br>Job: <a
href="http://www.ccl.net/jobs";
target="_blank">http://www.ccl.net/jobs</a> <br>Conferences:
<a href="http://server.ccl.net/chemistry/announcements/conferences/";
target="_blank">http://server.ccl.net/chemistry/announcements/conferences/</a><br><br>Search
Messages: <a href="http://www.ccl.net/chemistry/searchccl/index.shtml";
target="_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</a><br><br<br>
<a href="http://www.ccl.net/spammers.txt"; target="_blank">http://www.ccl.net/spammers.txt</a><br><br>RTFI: <a
href="http://www.ccl.net/chemistry/aboutccl/instructions/";
target="_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br><br><o:p></o:p></p></blockquote></div></div></div></body></html>