how to acknowedge original database papers (trac #134)

cloudy-bot commented 14 years ago

reported by: @CloudyLex

both the chianti and lambda databases have come with the authors asking that each use be acknowledged in any paper using cloudy. I think a print statement giving the original citation is triggered by the use of these databases.

we need to think of a fair way to do this in general. when these come into cloudy permanently they will be used all the time. there are other databases we use with less assertive authors. Examples are the Badnell and Meudon databases - we use Badnell all the time, and Meudon when atom H2 is used.

one option is to include a paragraph with citations to all major databases in the print citation command. The current approach of printing a comment in the header is ad hoc but ok for now. another option would be to include a list of databases in the main output towards the bottom.

Migrated from https://www.nublado.org/ticket/134

{
    "status": "closed",
    "changetime": "2019-02-04T13:20:38Z",
    "_ts": "1549286438224817",
    "description": "both the chianti and lambda databases have come with the authors asking that each use be acknowledged in any paper using cloudy.  I think a print statement giving the original citation is triggered by the use of these databases.\n\nwe need to think of a fair way to do this in general.  when these come into cloudy permanently they will be used all the time.  there are other databases we use with less assertive authors.  Examples are the Badnell and Meudon databases - we use Badnell all the time, and Meudon when atom H2 is used.\n\none option is to include a paragraph with citations to all major databases in the print citation command. The current approach of printing a comment in the header is ad hoc but ok for now.  another option would be to include a list of databases in the main output towards the bottom.\n",
    "reporter": "gary",
    "cc": "",
    "resolution": "fixed",
    "time": "2010-02-11T16:15:53Z",
    "component": "atomic/molecular data base",
    "summary": "how to acknowedge original database papers",
    "priority": "good to do",
    "keywords": "",
    "version": "trunk",
    "milestone": "",
    "owner": "",
    "type": "task"
}

cloudy-bot commented 14 years ago

@CloudyLex commented:

from Robin One precedent is how the source databases handle the authors from whom they get their source data. Do the primary authors get cited in all papers by the database owners themselves, just in an initial data overview, or only on the website?

The LAMDA front page says:

"If you use the data files in your work please refer to the publication by Schöier, F.L., van der Tak, F.F.S., van Dishoeck E.F., Black, J.H. 2005, A&A 432, 369-379 (astro-ph/0411110) introducing this data base. When individual molecules are considered, references to the original papers providing the spectroscopic and collisional data are encouraged."

...which suggests something like:

"If you use the results of Cloudy in your work please refer to the publication by Ferland et al. describing the code. When specific species or processes are considered, we encourage you to reference the original papers and databases which provided the underlying data."

and including the list of references to make this technically feasible.

It does seem likely someone reading a paper will want to be told the provenance of the data on which the conclusions rely in any material fashion. But it would be interesting to know what any journal would make of 15 pages of bibliography for a comprehensively referenced science paper ;-) The technicalities of how to handle data provenance robustly is generally an interesting topic...

cloudy-bot commented 14 years ago

@CloudyLex commented:

r3849 adds following print for databases in operation. the boilerplate starting (page 2) of each vol of hazy needs to be modified to say something along the lines of Robins' proposed script.

cloudy-bot commented 14 years ago

@CloudyLex commented:

Some databases used in this calculation: Many recombination coefficients are based on Badnell ApJS 167, 334 (2006) and Badnell et al A&A 406, 1151 (2003) and posted on the web sites http://amdpp.phys.strath.ac.uk/tamoc/RR/ and http://amdpp.phys.strath.ac.uk/tamoc/DR/. Much of the molecular emission data is from LAMDA (Schoeier et al 2005, A&A 432, 369-379) as accessed on Feb. 9, 2010. Much of the H_2 data is from Wrathmall & Flower 2007, JPhysB, 40 3221 Abgrall et al, 1994, Can. J. Phys., 72, 856 at http://molat.obspm.fr/index.php?page=pages/Molecules/H2/H2can94.php Please cite those papers were played a significant role in this calculation.

cloudy-bot commented 14 years ago

@CloudyLex commented:

we do two things: in the main printout there is an section that says:


 Some databases used in this calculation:
 Many recombination coefficients are based on Badnell ApJS 167, 334 (2006) and Badnell et al A&A 406, 1151 (2003) and posted on
      the web sites http://amdpp.phys.strath.ac.uk/tamoc/RR/ and http://amdpp.phys.strath.ac.uk/tamoc/DR/.
 Much of the molecular emission data is from LAMDA (Schoeier et al 2005, A&A 432, 369-379) as accessed on Feb. 9, 2010.
 Much of the ionic emission data is from CHIANTI. CHIANTI is a collaborative project involving the NRL (USA), the Universities of Florence (Italy) and Cambridge (UK), and George Mason University (USA). (Dere, K. P., Landi, E., Mason, H. E., Monsignori Fossi, B. C., & Young, P. R. 1997, A&AS, 125, 149) (Dere, K. P., Landi, E., Young, P. R., Del Zanna, G., Landini, M. & Mason, H. E. 2009, A&A, 498, 915) using version 6.0.1
.
 Please cite those papers that played a significant role in this calculation.

additionally the print citation command says


Cloudy is a research project that involves the creative efforts of many people.  It should be cited as follows:
Calculations were performed with version (trunk, r4159:4181M, experimental) of Cloudy, last described by Ferland et al. (1998).

The reference is:
Ferland, G. J., Korista, K. T., Verner, D. A., Ferguson, J. W., Kingdon, J. B., & Verner, E. M. 1998, PASP, 110, 761

In Latex this is:
\bibitem[Ferland et al.(1998)]{1998PASP..110..761F} Ferland, G.~J., Korista, K.~T., Verner, D.~A., Ferguson, J.~W., Kingdon, J.~B., \& Verner, E.~M.\ 1998, \pasp, 110, 761

 Some databases used in this calculation:
 Many recombination coefficients are based on Badnell ApJS 167, 334 (2006) and Badnell et al A&A 406, 1151 (2003) and posted on
      the web sites http://amdpp.phys.strath.ac.uk/tamoc/RR/ and http://amdpp.phys.strath.ac.uk/tamoc/DR/.
 Much of the molecular emission data is from LAMDA (Schoeier et al 2005, A&A 432, 369-379) as accessed on Feb. 9, 2010.
 Much of the ionic emission data is from CHIANTI. CHIANTI is a collaborative project involving the NRL (USA), the Universities of Florence
      (Italy) and Cambridge (UK), and George Mason University (USA). (Dere, K. P., Landi, E., Mason, H. E., Monsignori Fossi, B. C., & 
      Young, P. R. 1997, A&AS, 125, 149) (Dere, K. P., Landi, E., Young, P. R., Del Zanna, G., Landini, M. & Mason, H. E. 2009, A&A, 498,
      915) using version 6.0.1
.
 Please cite those papers that played a significant role in this calculation.

Matt checked with the chianti people, and Ryan with the lamda people, who were happy with this.

@CloudyLex changed resolution from "" to "fixed"
@CloudyLex changed status from "new" to "closed"

cloudy-bot commented 14 years ago

@CloudyLex commented:

Milestone Chianti lambda databases deleted

@CloudyLex changed milestone from "Chianti lambda databases" to "database infrastructure"

cloudy-bot commented 14 years ago

@peter-van-hoof-noaccount commented:

Milestone deleted

@peter-van-hoof-noaccount changed milestone from "database infrastructure" to ""

cloudy-astrophysics / bug-tracker-migration-test

how to acknowedge original database papers (trac #134) #136