Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Jürgen Bosch]

I guess I should just reply with “B.” since you replied with A. :-)

More seriously, 

Both A & B will need to have real hard proof of their claims as this is a real 
mess in which they got themselves into.

It seems as A despite not been hired by B succeeded in getting another 
position, which is good. B has taken advantage of his/her power position by not 
hiring A. He/she will find excuses why A was not a good fit blabla. From a 
moral perspective B sucks.
Just imagine what A in B’s lab could have achieved by having someone in the 
project already knowing everything about the dubious protein with a four letter 
PDB code. Must be one of those Ego’s out there without true team leadership 
skills.

Regarding the IP, that’s more difficult and again will require written evidence 
unless a patent has been filed and then that should be relatively easy and have 
the lawyers go after it.

All of these actions require extra attention and mental resources - is it worth 
for A? If you just want to be right, then read on to the bottom of this email.

Is the publication in C formally correct? Other than that A claims B took 
his/her coordinates to solve the structure. All that really counts is that the 
science around PDB  is correct.

From my own experience during my postdoc time, we had a paper under review for 
nine months. I know who one of the reviewers was because he copy-protected his 
comments in the pdf - unfortunately for him on a Mac your login user account is 
added per default to the pdf as creator, and that was just his plain name. 
The day after his paper was accepted at a different journal, ours was finally 
accepted as well. It is remarkable how some figures in his paper just adopt the 
same orientation and show the same things as ours. I never followed up on this 
as it was not worth my time. I will not reveal the authors names but I’m sure 
smart pople like you can write a little perl script to query the PDB in a 
meaningful manner.

This was more than 2 cents I wanted to add to this discussion and hopefully A 
does see the value in my last paragraph.

Jürgen 


__
Jürgen Bosch, Ph.D.
Division of Pediatric Pulmonology and Allergy/Immunology
Case Western Reserve University
2109 Adelbert Rd, BRB 835
Cleveland, OH 44106
Phone: 216.368.7565
Fax: 216.368.4223
https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology

> On Aug 21, 2019, at 4:49 AM, Anastassis Perrakis  wrote:
> 
> Something is unclear to me in the original question. What does “has used his 
> pdb for a publication” mean? Somebody used an entry already in the PDB? 
> Somebody used a “.pdb” coordinates file for publication (without “.mtz”)? 
> What was and is the relationship between A and B? 
> 
> In any case, assuming that A and B are not in talking terms (have you tried 
> through a mediator?), it is the director or designated ombudsperson of the 
> institute of A, that should review the case internally, and officially 
> contact the corresponding person of the institute of B. I can’t see what the 
> journal has to do with it, without a settlement between institutes. I also do 
> not consider a direct contact if A to the director of B appropriate. There 
> should be procedures for these cases. 
> 
> A. 
> 
> Sent from my iPhone
> 
> On 21 Aug 2019, at 10:12, Mark J van Raaij  > wrote:
> 
>> Dear Flemming,
>> 
>> As I understand it (I may be wrong), the final responsible institutions are 
>> those where the authors work. But as you say, they sometimes don't even 
>> reply - or they just may be very slow because they want to be really sure 
>> before committing to any answer.
>> 
>> But the journal has a responsibility also, to retract the paper if there is 
>> a serious suspicion the data were not obtained ethically. Of course, it may 
>> be difficult to prove ownership of a pdb file, if both authors claim 
>> ownership there is not really a way the journal can decide who is right. In 
>> my opinion, the journal should officially contact the institutions where the 
>> authors work to try and resolve this. The institutions may take the journal 
>> more seriously than a single researcher.
>> 
>> A generally respected institution that may advise on authorship disputes is 
>> COPE, Committee on Publication Ethics: https://publicationethics.org/ 
>> 
>> May also take a while though...
>> They have a database with anonymised examples of previously resolved 
>> disputes that may be helpful - you may find a similar situation on which 
>> they have "ruled". These are of course not legal rulings, but are considered 
>> by their members (most respectable journals) as a strong guideline.
>> This case may have similarities:
>> https://publicationethics.org/case/claim-stolen-data-and-demand-retractions 
>> 

Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Anastassis Perrakis]

Something is unclear to me in the original question. What does “has used his 
pdb for a publication” mean? Somebody used an entry already in the PDB? 
Somebody used a “.pdb” coordinates file for publication (without “.mtz”)? What 
was and is the relationship between A and B?

In any case, assuming that A and B are not in talking terms (have you tried 
through a mediator?), it is the director or designated ombudsperson of the 
institute of A, that should review the case internally, and officially contact 
the corresponding person of the institute of B. I can’t see what the journal 
has to do with it, without a settlement between institutes. I also do not 
consider a direct contact if A to the director of B appropriate. There should 
be procedures for these cases.

A.

Sent from my iPhone

On 21 Aug 2019, at 10:12, Mark J van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:

Dear Flemming,

As I understand it (I may be wrong), the final responsible institutions are 
those where the authors work. But as you say, they sometimes don't even reply - 
or they just may be very slow because they want to be really sure before 
committing to any answer.

But the journal has a responsibility also, to retract the paper if there is a 
serious suspicion the data were not obtained ethically. Of course, it may be 
difficult to prove ownership of a pdb file, if both authors claim ownership 
there is not really a way the journal can decide who is right. In my opinion, 
the journal should officially contact the institutions where the authors work 
to try and resolve this. The institutions may take the journal more seriously 
than a single researcher.

A generally respected institution that may advise on authorship disputes is 
COPE, Committee on Publication Ethics: https://publicationethics.org/
May also take a while though...
They have a database with anonymised examples of previously resolved disputes 
that may be helpful - you may find a similar situation on which they have 
"ruled". These are of course not legal rulings, but are considered by their 
members (most respectable journals) as a strong guideline.
This case may have similarities:
https://publicationethics.org/case/claim-stolen-data-and-demand-retractions

Best of luck,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


On 20 Aug 2019, at 17:45, Flemming Goery 
mailto:flemming_go...@hotmail.com>> wrote:

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming



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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Coker, Alun]

Dear Flemming,

This would be an intellectual property dispute. A is cleaning that B has used 
his IP without agreement. Most universities (and I assume other organisations) 
have IP policies that protect staff from having there IP stolen; the IP 
nominally belongs to the institution so the theft is legally from A's 
institution. I suggest that the correct procedure would be for A to contact 
their department responsible for IP to pursue B for IP theft.

Universities are highly sensitive to reputational damage so B's institution are 
likely not to back B if there is a reputational risk. Theft of IP would 
constitute a high risk of reputational damage.

All the best,

Alun

Dr Alun R. Coker
Associate Professor
University College London Division of Medicine
The Rayne Building
5 University Street
London
WC1E 6JF

Tel: 020 7679 6703 Ext 46703
Web: www.ucl.ac.uk/pxmed<http://www.ucl.ac.uk/pxmed>




From: Mark J van Raaij
Sent: Wednesday 21 August, 09:12
Subject: Re: [ccp4bb] need someone officially settle a pdb dispute for a 
publication
To: CCP4BB@JISCMAIL.AC.UK


Dear Flemming,

As I understand it (I may be wrong), the final responsible institutions are 
those where the authors work. But as you say, they sometimes don't even reply - 
or they just may be very slow because they want to be really sure before 
committing to any answer.

But the journal has a responsibility also, to retract the paper if there is a 
serious suspicion the data were not obtained ethically. Of course, it may be 
difficult to prove ownership of a pdb file, if both authors claim ownership 
there is not really a way the journal can decide who is right. In my opinion, 
the journal should officially contact the institutions where the authors work 
to try and resolve this. The institutions may take the journal more seriously 
than a single researcher.

A generally respected institution that may advise on authorship disputes is 
COPE, Committee on Publication Ethics: 
https://publicationethics.org/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublicationethics.org%2F&data=02%7C01%7C%7Cff30200e84e54aca4f7408d7260f50c8%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637019719533888373&sdata=QvZYG5V72vQU2HQuApB%2BjYJY%2FjZte2hDPBJALScpMvs%3D&reserved=0>
May also take a while though...
They have a database with anonymised examples of previously resolved disputes 
that may be helpful - you may find a similar situation on which they have 
"ruled". These are of course not legal rulings, but are considered by their 
members (most respectable journals) as a strong guideline.
This case may have similarities:
https://publicationethics.org/case/claim-stolen-data-and-demand-retractions<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublicationethics.org%2Fcase%2Fclaim-stolen-data-and-demand-retractions&data=02%7C01%7C%7Cff30200e84e54aca4f7408d7260f50c8%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637019719533898364&sdata=fIK7yCS9K2Vk6lojkkSQdpo2fVEpW9yDZPXdGFvL7u8%3D&reserved=0>

Best of luck,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


On 20 Aug 2019, at 17:45, Flemming Goery 
mailto:flemming_go...@hotmail.com>> wrote:

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7C%7Cff30200e84e54aca4f7408d7260f50c8%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637019719533898364&sdata=s6gdhcCw7GRINQp4C22X8JzALriiznlxRnmvt3gNLjw%3D&reserved=0>


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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Mark J van Raaij]

Dear Flemming,

As I understand it (I may be wrong), the final responsible institutions are 
those where the authors work. But as you say, they sometimes don't even reply - 
or they just may be very slow because they want to be really sure before 
committing to any answer.

But the journal has a responsibility also, to retract the paper if there is a 
serious suspicion the data were not obtained ethically. Of course, it may be 
difficult to prove ownership of a pdb file, if both authors claim ownership 
there is not really a way the journal can decide who is right. In my opinion, 
the journal should officially contact the institutions where the authors work 
to try and resolve this. The institutions may take the journal more seriously 
than a single researcher.

A generally respected institution that may advise on authorship disputes is 
COPE, Committee on Publication Ethics: https://publicationethics.org/ 

May also take a while though...
They have a database with anonymised examples of previously resolved disputes 
that may be helpful - you may find a similar situation on which they have 
"ruled". These are of course not legal rulings, but are considered by their 
members (most respectable journals) as a strong guideline.
This case may have similarities:
https://publicationethics.org/case/claim-stolen-data-and-demand-retractions 


Best of luck,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


> On 20 Aug 2019, at 17:45, Flemming Goery  wrote:
> 
> Dear All, 
> 
> A and B belong to 2 different institutes. A claimed B has used his pdb for a 
> publication in Journal C. Journal C did not give the retraction, but permit 
> complain related to the journal publication author issue, with the 
> prerequisite journal C did not have the authority on authorship dispute. Then 
> A has e-mailed to the institute head of B with academic misconduct by B as 
> claim, the institute head of B did not give reply.
> 
> In this situation, can A have the journal  authorship  dispute settled by a 
> neutral reviewer (Journal C view: you (A) need to reach out to the 
> institutions that have authority to adjudicate on such matters, as 
> investigation and adjudication on authorship claims falls outside the remit 
> of journal editors. )? Who are qualified as the neutral reviewer so that the 
> review decision can be submitted to Journal C?
> 
> If you believe you are qualified, or you know somebody or some organization 
> qualified, please let me know and I will introduce the issue to you by 
> separate e-mail (it is best not disseminated, am I right?)
> 
> Best regards.
> 
> Flemming
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 



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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Jürgen Bosch]

Can’t help you with this, however, I have a couple of PDB deposits that I did 
not publish on and if somebody took them and used my coordinates that’s fine as 
long as they cite the DOI affiliated with the deposition.

Now the question for you, were A and B collaborating on this? If so then 
there’s a different problem and indeed misconduct or at least not good practice 
by B.

Communication is a skill, that some people definitely need to learn.

Jürgen 
 

> On Aug 20, 2019, at 11:45 AM, Flemming Goery  
> wrote:
> 
> Dear All, 
> 
> A and B belong to 2 different institutes. A claimed B has used his pdb for a 
> publication in Journal C. Journal C did not give the retraction, but permit 
> complain related to the journal publication author issue, with the 
> prerequisite journal C did not have the authority on authorship dispute. Then 
> A has e-mailed to the institute head of B with academic misconduct by B as 
> claim, the institute head of B did not give reply.
> 
> In this situation, can A have the journal  authorship  dispute settled by a 
> neutral reviewer (Journal C view: you (A) need to reach out to the 
> institutions that have authority to adjudicate on such matters, as 
> investigation and adjudication on authorship claims falls outside the remit 
> of journal editors. )? Who are qualified as the neutral reviewer so that the 
> review decision can be submitted to Journal C?
> 
> If you believe you are qualified, or you know somebody or some organization 
> qualified, please let me know and I will introduce the issue to you by 
> separate e-mail (it is best not disseminated, am I right?)
> 
> Best regards.
> 
> Flemming
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 



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[ccp4bb] need someone officially settle a pdb dispute for a publication

[Flemming Goery]

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1