Editorial workflow in the Atlas

The Atlas editorial team stands in need of Section Editors (see http://atlasgeneticsoncology.org/BackpageAbout.html#EDITORIAL ) devoting 10% of their time for the Atlas.

The workflow detailed herein below applies when MSc students/workers are involved in the process. Indeed, a senior researcher will skim through the various steps described below. However a secretary's active watch on forthcoming papers from the various authors is needed (like an appointment calendar). Moreover, when the Atlas has evolved into a true database with an automated editorial process, many of these time consuming tasks will vanish.

For each of the themes included in the atlas (genes, leukemias, solid tumors, hereditary diseases involving increased risk of cancer, "deep insight" …), the editorial team is tasked with appraising the subjects (or "items") lending themselves to publication on the site.

As regards genes, for instance, using  a predefined list of the genes potentially implicated in cancer (a list determined by algorithms for different data bases by Philippe Dessen, the data base manager), the editorial team is initially tasked with verifying the implication (or non-implication) of these genes in carcinogenesis. With this in mind, they study the existing bibliography, primarily on the basis of the information contained in PubMed. They then endeavor to determine whether or not the published data suffice to justify a detailed written review.  

As regards the other themes (leukemias, solid tumors, hereditary diseases involving increased risk of cancer...), the bibliographic research is also carried out from PubMed, and also on specialized sites (Mitelman, Orphanet, OMIM, WHO, …). This research phase favors subjects for which enough recent publications are available to allow for high-quality reviews.

Finally, the editorial team decides whether or not a given subject will constitute an item justifying publication. After that, it is a matter of searching for and selecting the author in the best position to write this review.

Once a subject has been determined, the editorial team conducts a search of recent publications in view of choosing the author/the team in the best position to write something for the Atlas: their second appraisal. Concerning their choice, the following factors have got to be taken into account: number of publications by the author, the impact factor of his or her publications, and the author's status: clinician, hospital-based biologist, researcher. The author's disciplines are likewise taken into consideration: oncology, a specific organ, cytogenetic biology, molecular biology, cellular biology, physiopathology, etc. As regards teams, a multidisciplinary team will be preferred.

This is a highly sensitive step. According to the author chosen, the quality of the review is likely to vary, and its scientific orientation will be more or less fundamental or clinical.

Other selection criteria include: qualities of clarity in data presentation, synthesis and the use of schemas or medical imagery (in the broad sense of the word, including anatomopathology and chromosomes).
 

Along with the different items (genes, leukemias, solid tumors...), all important data on the authors are conserved in dedicated files.

And for each gene, the spreadsheets inventory information on its implication, as well as all other information deemed useful for future research (authors to be contacted, their contact information, e-mail exchanges, agreement to write an article, speed in production, and subjects to be reserved for a given author...). Totally indispensable, the spreadsheets are of concrete use during each phase of the work. They need to be ergonomic, and evolve according to changing needs. 

For each theme in the Atlas (Genes, Leukemias, Solid Tumors, Hereditary Diseases involving increased risk of cancer, "deep Insights", Teaching Chapters), there exists a dedicated spreadsheet.

Each spreadsheet provides a list of the subjects studied, the relevant dates, as well as the subjects to be studied, for which the right authors remain to be found.

The spreadsheets are updated daily, and new, potentially interesting subjects are added periodically. This supplementary material is enriched by readings of articles from the literature and by analysis of the articles received by the Atlas.   

Each subject is designated by a specific and numbered identifier facilitating the establishment of internal links as the files are being edited.

Possible duplicate files are regularly sought out and subjected to analysis, and the spreadsheets are consequently "cleaned".  

For an example, see below: Extracts from the "Genes" spreadsheet, which contains 9000 lines.

The authors are contacted through a common e-mail account using predetermined contact e-mail coordinates.

The e-mails are sent once a week, at the beginning of the week, as it has been observed that the highest response rate occurs at that time. On the same token, some times of the year are not conducive to soliciting authors who tend to be busy with applications for grants ... or on holiday. These periods are avoided as much as possible.

When an author fails to answer, he is re-contacted two or three times. If, after that, he still fails to answer, another author is sought out...

Author response statistics: 55% of the authors do not respond to the invitation; 25% of them refuse; 20% agree.

When authors refuse or do not respond, the process of searching for the right author is reinitiated. If no other author can or will write the requested review, the team will wait for new research to be published..

When, on the other hand, an author accepts, the team consults him on the time frame he thinks he shall need prior to sending his completed article. The publishing flow is thereby managed, both for the Internet site and the PDF journal. A model of writing for the review is given the author, who concomitantly receives relevant editorial information.

Quite frequently, articles fail to arrive within the allotted time. The status of ongoing articles has got to be regularly monitored, and reminder notes need to be sent. 

It also often happens that notwithstanding an initially positive response, authors do not respond to reminder notes, or else they withdraw from the project. In those cases, search for the right author resumes.

Assistance for authors: Quite frequently, authors ask questions (deadlines , explanations pertaining to various details...) that call for timely responses.

 Once the article has been received, the completed worksheet is registered on a common server.

The information is also recorded on common spreadsheets, in a common notebook dedicated to the editors' ongoing activities; it is also displayed on wall calendars providing overall perspective on publication flows.

With these calendars, the editorial team can rapidly apprise itself of a possible lack of articles for the PDF journals and try to optimally manage the flow of arriving articles. Unfortunately, given the fact that the authors are the ones who determine their sending dates, substantial variations in publication flow may come to exist, and not be easy to manage.

The articles received are reread by internal referees; 97% of them (in fact all the articles, except for clinical case reports) are reviews of the literature written at the request of the Atlas editorial board; they are known as "commissioned papers". It should be noted that the authors were preselected according to rigorously applied criteria preliminarily to their writing of an article. Following receipt, the process of rereading and assessment of articles is implemented by the Atlas editorial board. It should also be noted that as the process draws to a close, the board member having chosen the subject (and subsequently the author himself) possesses a precise overall vision as to what the article is supposed to produce (quantity of knowledge in molecular biology or clinical research on a given gene...).     

Articles that do not correspond to the publication criteria or that do not provide a sufficiently detailed report on the knowledge available on the subject are sent back for revision. The editorial team remains vigilant, and about 20% of the articles submitted are indeed sent back for revision. It is often necessary to send reminders to the authors, before receiving the revised version (loss of time).  

The clinical case studies in hematology (the remaining 3%) are subjected to an external assessment process involving 4 or 5 experts, while the final decision is made by the Atlas editor-in-chief. Practically all the clinical case studies are reviewed by the authors at least one time prior to publication; only 8% are immediately accepted, 68% are accepted following revision, and 24% of the articles having been submitted are finally refused.
 

Once the articles have been accepted, they are processed so that they can be placed on line by the data base manager.

The articles are to be formatted according to a strictly applied computational model in order to be properly handled by the scripts of the data base manager (see, as an example, the form below).

The text must be painstakingly reread so as to correct possible mistakes (typos, grammar, spelling...),   and each bibliographical reference cited in the next has got to be verified and corrected (if need be).

The article header (the different tags or tracking devices allowing for indexing of the form in different parts of the data base in accordance with different criteria) must be carefully filled out, using the metadata contained in the article. The metadata will permit the data base manager to integrate the form within the site so that it can be inventoried with regard to the dedicated lists.  

The articles in the Atlas must follow a predetermined model; each paragraph of the review must be included within the tags, and the text must be formatted according to a computer encoding system. Special characters (accent marks, Greek letters, symbols…ex: integrin ανβ3) must be coded in the HTML format so that their posting on the website be correct. 

In the text itself, all potential internal links to other items contained in the Atlas (genes, leukemias, solid tumors...) must be identified, and internal links created in such a way that readers are directed, if they wish, to other articles in the Atlas. New subjects for the Atlas are often found while the forms are being processed, and added to the shared spreadsheets.  

Most often, the bibliography contains 50 to 100 references, and it has got to be processed in a predetermined format.

The articles also contain images, which are processed by Photoshop software. More often than not, the size of the images requires rectification, and the background of the image has got to be rendered transparent. Moreover, the text may need rewriting when it is too blurry or has been degraded due to the change in size.  

Once processing of the worksheet has been completed, it is put through a simulator so as to verify the correctness of its formatting, and also so as to make sure that no component remains invisible, as happens when a closing tag such as > is forgotten. 

The file and the attached images are then sent for validation to Jean-Loup Huret, the editor-in-chief, and subsequently to the data base manager for uploading or posting on line.  

"Deep Insight" and "Educational items" constitute special cases. As these files are "free format" and do not correspond to a precise model, they are directly processed using specialized software (the Dreamweaver website-editing software) in the HTML format. For these files, it is necessary to carry out all coding and page layout in HTML.

Example below : Partial formatting of an article: In the example given below, any and all parts of the text in color are subjected to special processing.

BEGIN_HEADER

FILENAMESH3PXD2AID45995ch10q24.txt

CLASSE GENE

ID45995

LOCUSID

TRI_PAR_CHROMOSOME10

TRANSLOC t(10;10)(q24;q24) SH3PXD2A/OBFC1

TRANSLOC t(10;13)(q24;q14) SH3PXD2A/RB1

FUSION_GENESH3PXD2A/OBFC1

FUSION_GENESH3PXD2A/RB1

CATEGORYCytoskeleton

END_HEADER

etc..

etc...

FUNCTIONTKS5 was initially identified as a substrate for <CC: TXT:SRC ID: 448> (Lock et al., 1998), and was subsequently shown to play a critical role in invadosome formation in multiple cell types (Courtneidge, 2011; Murphy and Courtneidge, 2011; Paz et al., 2013). <BR>

FUNCTIONFull-length TKS5 functions as an adaptor for recruiting other proteins to the cell membrane for invadosome formation. The recruitment of TKS5 to the cell membrane depends on its PX domain and phosphorylation by Src (Abram et al., 2003). It has been proposed that phosphorylation of TKS5 releases its PX domain from intramolecular interaction and allows TKS5 to bind to cell membrane phosphatidylinositol lipids, such as phosphatidylinositol-3,4-bisphosphate (PI(3,4)P₂) (Abram et al., 2003; Oikawa et al., 2008). At the cell membrane, TKS5 is thought to interact with multiple components of invadosomes either directly or indirectly, and thereby mediates invadosome formation and maturation (Sharma et al., 2013). These interacting partners includes adaptor proteins and actin regulatory proteins, such as <CC: TXT:NCK1 ID:41505>, <CC: TXT:NCK2 ID:52582>, <CC: TXT:GRB2 ID: 386>, <CC: TXT: CTTN ID: 369> (Cortactin), <CC: TXT: WASL ID: 42803> (N-WASP), <CC: TXT: ACTR2ID: 49744<CC: TXT: ACTR3ID:46303> (Arp2/3) complex, and <CC: TXT: ARHGAP35 ID: 52237> (p190RhoGAP) (Crimaldi et al., 2009; Oikawa et al., 2008; Stylli et al., 2009).<BR>

FUNCTION TKS5 also interacts with <CC: TXT:NOXA1 ID:41563> and <CC: TXT: CYBA ID: 43882> (p22phox), which are components of the NADPH oxidase complex, and thereby promotes reactive oxygen species (ROS) production by NOX enzymes at invadosomes (Diaz et al., 2009; Gianni et al., 2010; 2009).ROS have been shown to facilitate invadosome formation by maintaining or amplifying the phosphorylation of TKS5. As such, TKS5 is thought to promote invadosome formation via ROS in a positive feedback loop.<BR>

FUNCTION Finally, TKS5 has also been shown to interact with members of the ADAM family metalloproteases, specifically <CC: TXT:ADAM12 ID:44084>, <CC: TXT:ADAM15 ID:46345>, <CC: TXT:ADAM19 ID:46837>(Abram et al., 2003). It is believed that Tks5 recruits theses proteases to the invadosome foci for processing growth factors and regulating cell motility. For example, ADAM12 has been shown to promote ectodomain shedding of <CC: TXT:HBEGF ID: 40369> (heparin-binding EGF-like growth factor) and enhance invadopodia formation in cancer cells (Diaz et al., 2013). <BR>

etc...

Article upload takes place virtually every week, and for each article, it has to be verified.   Also to be verified: Has the article been correctly indexed in  the dedicated lists? Has the article been correctly displayed? .

Before a thank-you e-mail is sent to the authors of a review, their bibliographies are searched so as to see if they could possibly be tasked with another review. If this is the case, they are asked whether or not they would be interested in pursuing their collaboration.   

The author is given the address at which he can find his review on the Atlas site.

Prior to each issue, the editor in charge of the journal is tasked with creating the table of contents and scrupulously selecting the articles to be published. This is because publishing workflow is highly fluctuating, and consequently demands "hands-on" management.

A tool for the future data base carrying out initial formatting of the articles and editing the table of contents provides assistance in the page layout of the PDF journal.

In each issue, page layout is a sensitive matter. It is performed article by article, and has got to be done in such a way that a given issue is harmonious and satisfactorily balanced; moreover, image management must ensure maximal quality.

Once the journal is formatted and paginated, it is validated by the editor-in-chief.

The issue is then sent to the INIST-CNRS for finalizing of the PDF. The INIST editors recover the meta-data for the articles and associate them with the issue. They are also tasked with assigning the DOI (digital object identifier) for each article that will serve as its single identification number.  

For back-up purposes, this final PDF is registered on the future data base.

Once all of the above steps have been carried out, the authors are contacted anew and informed of the publication of their articles in the journal and the link to the latter in PDF with which they are being provided.  

 The above percentages are subject to modification according to editorial needs and the fluctuating importance of certain tasks.

Again, we want to make it clear that the workflow detailed herein applies when MSc students/workers are involved in the process. Indeed, a senior researcher will skim through the various steps. However a secretary's active watch on forcoming papers is needed. Moreover, when the Atlas has evolved into a true database with an automated editorial process, many of these time consuming tasks will vanish.

The Atlas can run with:

- an Editor in Chief (20% full-time) + secretary (2-5%).

- Section Editors (5- 10% full-time) + secretary (1%).

- a Bio-computer specialist (10% full time).

- .. and as many good authors as possible !

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