Welcome to SciELO PC Programs’ documentation!¶

SciELO PC Programs is a set of tools of SciELO Methodology. They run on Windows and are used to manage journals, issues and articles data, in order to prepare them to the data processing which generates the website (SciELO Site).

Download¶

Download by FTP

server: ftp.scielo.br
user: produtos-scielo
password: produtos@scielo

Requirements¶

JAVA

PYTHON 2.7.x

How to install¶

Download the last version
Run the program
Follow the instructions given in each screen
Configure

application’s name

Examples: SciELO Brazil, SciELO Chile, SciELO v4.0, etc., or just SciELO.

URL

production website address Example: www.scielo.br

destination data folder

folder which have serial folder

Select the programs you want to install in your computer, considering if it is the local server or the markup computer.

Programs for local server¶

Code Manager: program to manager tables of codes/labels. For example, countries table: BR (code) and Brazil (label)
Title Manager: program to manager journal data that are part of the collection, their issues and sections of table of contents
Converter: program responsible for loading the CDS / ISIS databaseusing complete text documents previously marked
Markup: program to identify each bibliographic element on articles and texts
SGML Parser: program to identify possible markup errors on the marked files. It is always installed.
XML SciELO: program (optional) to create XML format accepted byPubMed and ISI

Programs for Markup Computer¶

Markup: program to identify each bibliographic element on articles and texts
SGML Parser: program to identify possible markup errors on the marked files. It is always installed.

Note: Markup - automata files are examples of automatas. Its installation is optional.

For local server installation, set the environment variable BAP as OS23470a.
By Windows menu go to: Control Panel -> Performance and Maintenance -> System -> Advanced Settings -> Environment variables.
Check if the variable already exists.
If it does not, click New and enter the data.
Install Java and set its location in PATH.
The shortcurts are created to administrator user, so copy the shortcuts for all the users.
Give the write permission to non-admin users on C: (for Parser usage) and all the folders below the bin folder, because the programs generate files in these folders.
Select the C: drive and click on Properties option.

Open the security tab

Select users (common users)

Click on Edit button

Check all the permissions. Then click on Apply to set the permissions.

Local server¶

It’s a Windows machine where the PC Programs and SciELO website (local site) run.

SciELO collection or instance¶

SciELO Collection or instance is a website generated using SciELO Methodology, including the ones which do not use SciELO in their website name.

Examples of collections or instances: SciELO Brazil, SciELO Chile, SciELO Salud Pública, Rev@Enf, etc.

Types of issues¶

regular or supplement: number formed by articles and texts
ahead: manuscripts that were approved by editorial board but they are not in a definitive issue. There is an ahead number by year.
review/provisional: number whose purpose is to group accepted articles which are still under review, leaving only their metadata published. There is a review number by year. Note: at the site the name adopted is provisional
pr (press release): number whose purpose is to group the press releases texts of a number or article. There is a pr number by issue.

Sequential number¶

The sequential number is a number formed by year (YYYY), followed by a number that gives the issue’s order within a year.

This number has two purposes:

order of the issue within a year in the “all issues” page of the website
forming PID. It is strongly recommendable DO NOT MODIFY THIS ITEM if the issue has already been published on the website.

By convention, the sequential number is:

ahead = 50
review/provisional = 75
pr = from 100

Example:

v.40 n.1	20091
v.40 n.2	20092
v.40 suppl.	20093
v.40 suppl.2	20094
v.40 n.2 suppl.1	20095
ahead	200950
review	200975
v.40 n.1 pr	2009100

Folders Structure¶

SciELO PC Programs package has the folders:

bin and xml_scielo, for programs
serial, for data

You can install them in the same or different folders. BUT by CONVENTION, we recommend C:\scielo\bin and c:\scielo\serial.

Examples of the same folder:

c:\scielo\bin… and c:\scielo\serial
d:\scielo_v4.0\bin and d:\scielo_v4.0\serial

Examples of different folders:

c:\scielo\bin… e d:\scieloserial
d:\scielo-programs\bin… and d:\scielo-dataserial

Programs folder¶

It contains the programs. E.g.: \scielo\bin

Data folder¶

e.g.: \scielo\serial

In this folder are all data, all the databases.

title: it contains data records related to the journal

section: it contains data records of sections of the table of contents

issue: it contains the records of journal’s issues

code: it contains tables of codes/labels

PubMed: is used in order to archive the XML files sent to PubMed

ISI: is used in order to archive the XML files sent to ISI

several Journal’s folder: which contains the issues of the journal

Journal’s folder¶

e.g.: \scielo\serial\<acronym>

It contains several folders, each one for each issue of the journal.

Issue folder¶

It contains folders like:

markup: articles and text files, with markup
body: articles and text files, original, no markup
pdf: articles and texts in PDF format
img: image files extracted from the PDF files
base: the databases generated by Converter from the files of markup and body folders.

There are rules to name theses folders:

Folders for regular numbers and supplements: v, followed by the volume number, s, followed by the supplement to volume, n, followed by the number issue, s, followed by the supplement number
Examples:
v31n1 (volume 31, number 1)

v31n1s1 (volume 31, number 1, supplement 1)

v31n1s0 (volume 31, number 1, supplement)

v31s0 (volume 31, supplement)

v31s1 (volume 31, supplement 1)

v31nspe (volume 31, special number)

v31n3a (volume 31, number 3A)
Review / Provisional’s and ahead’s folder: publication’s year, n, followed by the word review or ahead
Examples:
2009nahead

2010nreview
Ex-review/provisional’s and ex-ahead’s folders: ex-, followed by publication’s year, n followed by the number. NOTE: Converter creates these folders, because it is only way to control data files which were review/provisional and/or ahead once.
Examples:
ex-2009nahead

ex-2010nreview
Press releases’ folders: it follows the same rules of regular numbers and supplements, review / provisional and ahead, adding pr at the end of the file name.
Examples:
v31n1pr (press release of volume 31, number 1)

v31n1s1pr (press release of volume 31, number 1, supplement 1)

v31n1s0pr (press release of volume 31, number 1, supplement)

v31s0pr (press release of volume 31, supplement)

v31s1pr (press release of volume 31, supplement 1)

v31nspepr (press release of volume 31, special number)

v31n3apr (press release of volume 31, number 3A)

Local website¶

SciELO Website for Windows.

Programs for local server¶

Code Manager¶

single-user program,
Visual Basic
used on local server
manage the tables of codes and values used by all the programs of SciELO Methodology.

There are tables which contents are rarely changed, for example, languages. There are tables where the content is customizable for each collection. Currently: sponsor, markup center.

The table of subject areas was customizable. But now, it is required all the collections of the SciELO Network use the same table.

This program is only used if it is necessary to change data of the customizable tables.

Opening the program¶

To open the program, use the Windows menu, select SciELO, then Code Manager

Managing the tables¶

Select Files

Restricted Area is used only by the developers of SciELO methodology. It is password protected.
Customizing Tables is to manage the customizable tables.

Accessing a table¶

Select one of the tables, clicking the button …

The data of the tables will be presented in the format: code | label in Portuguese | Spanish | English.

Removing a row of the table¶

Select a row to delete. Its data will be presented at code and labels fields of each language.
Click on Remove button.
Click on Save button

Updating a row of the table¶

Select a row to update. Its data will be presented at code and labels fields of each language.
Click on Update button.
Click on Save button

Creating a new row¶

Fill in the fields: code and label of each language

Technical information¶

Code database¶

ISIS database. One record by table.

Field 1: Subfield *: table name Subfield l, optional: language
Field 2: Subfield c: code Subfield v: value

NewCode database¶

Same structure of code database, but the records corresponding to the editable tables are the only records that would be different.

Code database Content¶

doctopic¶

code	value
ab	abstracts
ax	annex
an	announcements
sc	brief communication
co	comments
cr	case report
ct	clinical trial
ed	editorial
in	interview
le	letter
mt	methodology
oa	original article
pv	point-of-view
pr	press release
rc	recount
rn	research note
ra	review article
tr	technical report
up	update

role¶

code	value
nd	Not defined
coord	coordinator
ed	publisher
org	organizer
tr	translator

standard¶

code	value
iso690	iso 690/87 - international standard organization
nbr6023	nbr 6023/89 - associação nacional de normas técnicas
other	other standard
vancouv	the vancouver group - uniform requirements for manuscripts submitted to biomedical journals
apa	American Psychological Association

ccode¶

code	value
bjce	brazilian journal of chemical engineering
bjg	brazilian journal of genetics
bjmbr	brazilian journal of medical and biological research
bjp	brazilian journal of physics
conicyt	Comisión Nacional de Investigación Científica y Tecnológica
dados	dados - revista de ciências sociais
br1.1	scielo/bireme
infomed	InfoMed
jbchs	journal of the brazilian chemical society
jbcos	journal of the brazilian computer society
mioc	memórias do instituto oswaldo cruz
rbcs	revista brasileira de ciência do solo
rbgeo	revista brasileira de geociências
rimtsp	revista do instituto de medicina tropical de são paulo
rsp	revista de saúde pública

literature type¶

code	value
C	Conference
M	Monograph
MC	Conference papers as Monograph
MP	Project papers as Monograph
MPC	Project and Conference papers as monograph
MS	Monograph Series
MSC	Conference papers as Monograph Series
MSP	Project papers as Monograph Series
N	Document in a non conventional form
NC	Conference papers in a non conventional form
NP	Project papers in a non conventional form
P	Project
S	Serial
SC	Conference papers as Periodical Series
SCP	Conference and Project papers as periodical series
SP	Project papers as Periodical Series
T	Thesis and Dissertation
TS	Thesis Series

treatment level¶

code	value
am	analytical of a monograph
amc	analytical of a monograph in a collection
ams	analytical of a monograph in a serial
as	analytical of a serial
c	collective level
m	monographic level
mc	monographic in a collection
ms	monographic series level

status¶

code	value
?	Unknown
C	Current
D	Ceased
R	Reports only
S	Suspended

month¶

code	value
1	Jan.
2	Feb.
3	Mar.
4	Apr.
5	May
6	June
7	July
8	Aug.
9	Sept.
10	Oct.
11	Nov.
12	Dec.

date¶

code	value
Jan.	January
Feb.	February
Mar.	March
Apr.	April
May	May
Jun.	June
July	July
Aug.	August
Sept.	September
Oct.	October
Nov.	November
Dec.	December

country¶

code	value
AF	Afghanistan
AL	Albania
DZ	Algeria
AS	American Samoa
AD	Andorra
AO	Angola
AQ	Antarctica
AG	Antigua
AR	Argentina
AU	Australia
AT	Austria
BS	Bahamas
BH	Bahrain
BD	Bangladesh
BB	Barbados
BE	Belgium
BZ	Belize
BM	Bermuda
BT	Bhutan
BO	Bolivia
BW	Botswana
BV	Bouvet Island
BR	Brazil
VG	British Virgin Islands
BN	Brunei
BG	Bulgaria
BU	Burma
BI	Burundi
BY	Byelorussian RSS
CM	Cameroon
CA	Canada
CV	Cape Verde
CF	Central African Rep.
TD	Chad
CL	Chile
CN	China
CO	Colombia
CG	Congo
CR	Costa Rica
CU	Cuba
CY	Cyprus
CS	Czechoslovakia
DK	Denmark
DM	Dominica
DO	Dominican Republic
NQ	Dronning Maud Land
EC	Ecuador
EG	Egypt
SV	El Salvador
ET	Ethiopia
FK	Falkland Islands(Malvinas)
FJ	Fiji
FI	Filand
FR	France
GF	French Guiana
PF	French Polynesia
GA	Gabon
DD	German Democratic Republic
DE	Germany, Federal Republic
GH	Ghana
GI	Gibraltar
GR	Greece
GL	Greenland
GD	Grenada
GP	Guadeloupe
GU	Guam
GT	Guatemala
GC	Guinea Ecuatorial
GN	Guinea
GW	Guinea-Bissau
GY	Guyana
HT	Haiti
HN	Honduras
HK	Hong Kong
HU	Hungary
IS	Iceland
IN	India
ID	Indonesia
IR	Iran
IQ	Iraq
IE	Ireland
CX	Isla de Navidad
JT	Isla Johnston
NU	Isla Niue
WK	Isla Wake
PU	Islands Miscellaneous
CT	Islas Canton y Enderbury
CC	Islas Cocos (Keeling)
CK	Islas Cook
FO	Islas Feroe
HM	Islas Heard y Mc Donald
MI	Islas Midway
PN	Islas Pitcairn
SB	Islas Salomón Británico
SJ	Islas Svalbard y Jan Mayen
TK	Islas Tokelau
WF	Islas Wallis y Futuna
IL	Israel
IT	Italy
YU	Iugoslavia
CI	Ivory Coast
JM	Jamaica
JP	Japan
JO	Jordan
KM	Kamoras Islands
KH	Kampuchea Democrática
KY	Kayman Islands
KE	Kenya
KD	Korea, Democratic People’s
KP	Korea, Democratic People’s
KR	Korea, Republic of
KW	Kuwait
LD	Lao People’s Democratic
LB	Lebanon
LS	Lesotho
LR	Liberia
LY	Libyan
LI	Liechtenstein
LU	Luxembourg
MO	Macau
MG	Madagascar
MW	Malawi
MY	Malaysia
MV	Maldivas
ML	Mali
MT	Malta
MQ	Martinique
MR	Mauritania
MU	Mauritius
MX	Mexico
MC	Monaco
MN	Mongolia
MS	Montserrat
MA	Morocco
MZ	Mozambique
NA	Namibia
NR	Nauru
NP	Nepal
NL	Netherlands
AN	Netherlands Antilles
NC	New Caledonia
NZ	New Zealand
NI	Nicaragua
NE	Niger
NG	Nigeria
NF	Norfolk Island
NO	Norway
NH	Nuevas Hébridas
OM	Oman
PC	Pacific Islands
PK	Pakistan
PA	Panama
PG	Papua New Guinea
PY	Paraguay
PE	Peru
PH	Philippines
PL	Poland
PT	Portugal
PR	Puerto Rico
QA	Qatar
LA	Republic
RE	Réunion
RO	Romania
RW	Rwanda
PM	Pedro y Miguelón
LC	Saint Lucia
VC	Saint Vincent
WS	Samoa
KN	San Cristóbal-Nieves-Anguila
SM	San Marino
ST	Sao Tome and Principe
SA	Saudi Arabia
SC	Seichelles
SN	Senegal
SL	Sierra Leone
SK	Sikkim
SG	Singapur
SO	Somalia
ZA	South Africa
ES	Spain
LK	Sri Lanka
SH	St. Helena
SD	Sudan
SR	Suriname
SZ	Swaziland
SE	Sweden
CH	Switzerland
SY	Syrian Arab Republic
TW	Taiwan
TZ	Tanzania
TH	Thailand
TG	Togo
TO	Tonga
TT	Trinidad and Tobago
TN	Tunisia
TR	Turkey
TC	Turks and Caicos Islands
UG	Uganda
UA	Ukrainian RSS
AE	United Arab Emirates
GB	United Kingdom
US	United States
UP	United States Pacific
HV	Upper Volta
SU	URSS
UY	Uruguay
VU	Vanuatu
VA	Vatican City State
VE	Venezuela
VN	Viet Nam
EH	Western Sahara
YE	Yemen
YD	Yemen, Democratic
ZR	Zaire
ZM	Zambia
nd	Not defined

publication level¶

code	value
CT	Scientific/technical
DI	Divulgation

alphabet of title¶

code	value
A	Basic Roman
B	Extensive Roman
C	Cirillic
D	Japanese
E	Chinese
K	Korean
O	Another alphabet

language¶

code	value
en	English
pt	Portuguese
es	Spanish
af	Afrikaans
ar	Arabic
bg	Bulgarian
ch	Chinese
cs	Czech
da	Danish
nl	Dutch
eo	Esperanto
fr	French
de	German
gr	Greek
he	Hebrew
hi	Hindi
hu	Hungarian
in	Indonesian
ia	Interlingua
ie	Interlingue
it	Italian
ja	Japanese
ko	Korean
la	Latin
no	Norwergian
pl	Polish
ro	Romanian
ru	Russian
sa	Sanskrit
sh	Serbo-Croat
sk	Slovak
sn	Slovenian
sv	Swedish
tr	Turkish
uk	Ukrainian
ur	Urdu
zz	Other
gl	Galician
eu	Basque
ca	Catalan

frequency¶

code	value
?	Unknown
A	Annual
B	Bimonthly (every two months)
C	Semiweekly (twice a week)
D	Daily
E	Biweekly (every two weeks)
F	Semiannual (twice a year)
G	Biennial (every two years)
H	Triennial (every three years)
I	Three times a week
J	Three times a month
K	Irregular (known to be so)
M	Monthly
Q	Quarterly
S	Semimonthly (twice a month)
T	Three times a year
W	Weekly
Z	Other frequencies

indexing coverage¶

code	value
BA	Biological Abstracts
EM	Excerpta Medica
IM	Index Medicus
LL	LILACS
SP	Salud Publica

acquisition priority¶

code	value
1	Indispensable
2	Dispensable because exists in the Country
3	Dispensable because exists in the Region

state¶

code	value
AC	Acre
AL	Alagoas
AM	Amazonas
AP	Amapá
BA	Bahia
CE	Ceará
DF	Distrito Federal
ES	Espírito Santo
FN	Fernando de Noronha
GO	Goiás
MA	Maranhão
MG	Minas Gerais
MS	Mato Grosso do Sul
MT	Mato Grosso
PA	Pará
PB	Paraíba
PE	Pernambuco
PI	Piauí
PR	Paraná
RJ	Rio de Janeiro
RN	Rio Grande do Norte
RO	Rondônia
RR	Roraima
RS	Rio Grande do Sul
SC	Santa Catarina
SE	Sergipe
SP	São Paulo

article status¶

code	value
1	Available

stitle¶

code	value
Acta Cir. Bras.	Acta Cirurgica Brasileira
Bragantia	Bragantia
Braz. J. Chem. Eng.	Brazilian Journal of Chemical Engineering
Braz. J. Genet.	Brazilian Journal of Genetics
Braz J Med Biol Res	Brazilian Journal of Medical and Biological Research
Braz. J. Phys.	Brazilian Journal of Physics
Cad. CEDES	Cadernos CEDES
Cad. Saúde Púbica	Cadernos de Saúde Pública
Ci. Inf.	Ciência da Informação
Ciênc. Tecnol. Aliment.	Ciência e Tecnologia de Alimentos
DELTA	DELTA: Documentação de Estudos em Lingüística Teórica e Aplicada
Dados	Dados
Educ. Soc.	Educação & Sociedade
Genet. Mol. Biol.	Genetics and Molecular Biology
Venom. Anim. Toxins	Journal of Venomous Animals and Toxins
Braz. Chem. Soc.	Journal of the Brazilian Chemical Society
Braz. Comp. Soc.	Journal of the Brazilian Computer Society
Mem. Inst. Oswaldo Cruz	Memórias do Instituto Oswaldo Cruz
Pesq. Vet. Bras.	Pesquisa Veterinária Brasileira
Psicol. USP	Psicologia USP
Rev. bras. Bot.	Revista Brasileira de Botânica
Rev Bras Cir Cardiovasc	Revista Brasileira de Cirurgia Cardiovascular
Rev. bras. Ci. Solo	Revista Brasileira de Ciência do Solo
Rev. bras. Ci. Soc.	Revista Brasileira de Ciências Sociais
Rev. bras. Geocienc.	Revista Brasileira de Geosciences
Rev. bras. Hist.	Revista Brasileira de História
Rev Panam Salud Publica	Revista Panamericana de Salud Pública
Rev. Fac. Educ.	Revista da Faculdade de Educação
Rev. Microbiol.	Revista de Microbiologia
Rev Odontol Univ São Paulo	Revista de Odontologia da Universidade de São Paulo
Rev. Saúde Pública	Revista de Saúde Pública
Rev. Inst. Med. trop. S. Paul	Revista do Instituto de Medicina Tropical de São Paulo
Sci. agric.	Scientia Agricola
Salud pública Méx	Salud Pública de México

illustrative material type¶

code	value
nd	no illustrative material
ilus	figure
gra	graphic
map	map
tab	table

version¶

code	value
3.1	3.1
4.0	4.0

from¶

code	value
00000000	00000000

to¶

code	value
00000000	00000000

keyword priority level¶

code	value
m	main
s	secondary

toccode¶

code	value
1	title
2	sectitle

scheme¶

code	value
nd	No Descriptor
decs	Health Science Descriptors

ftp¶

code	value
art	article based - a PDF file for each article
iss	issue based - a PDF file for each issue
na	Not Available

usersubscription¶

code	value
na	Not Available
reg	Electronic Registration
sub	Regular Subscription

id¶

code	value
nd	Not defined

stud area¶

code	value
Agricultural Sciences	Agricultural Sciences
Applied Social Sciences	Applied Social Sciences
Biological Sciences	Biological Sciences
Engineering	Engineering
Exact and Earth Sciences	Exact and Earth Sciences
Health Sciences	Health Sciences
Human Sciences	Human Sciences
Linguistics, Letters and Arts	Linguistic, Literature and Arts

rid¶

code	value
nd	Not defined

dateiso¶

code	value
00000000	00000000

count¶

code	value
0	0

pii¶

code	value
nd	Not defined

pages¶

code	value
0-0	0-0

issue status¶

code	value
1	Available
0	Not available
2	Partial available

idiom interface¶

code	value
es	Spanish
pt	Portuguese
en	English

table of contents¶

code	value
en	Table of Contents
pt	Sumário
es	Sumario

orgname¶

code	value
nd	nd

no¶

code	value
0	0

scielonet¶

code	value
1	SciELO Brasil
2	SciELO Chile
3	SciELO Salud Pública
4	SciELO BEEP
5	SciELO Ecler
6	SciELO Cuba
7	SciELO Colombia
8	SciELO Costa Rica
9	SciELO Uruguay
10	SciELO Argentina
11	SciELO Biodiversidade
12	SciELO Bolivia
13	SciELO España
14	SciELO Jamaica
15	SciELO México
16	SciELO Perú
17	SciELO Portugal
18	SciELO Venezuela
19	SciELO Adolec
20	SciELO Social Sciences
21	SciELO Paraguay
22	SciELO Ecuador
23	SciELO Caribbean
24	SciELO South Africa

issn type¶

code	value
CDROM	CD-ROM ISSN
DISKT	Diskette ISSN
ONLIN	On line ISSN
PRINT	PRINT ISSN

orgdiv1¶

code	value
nd	nd

orgdiv2¶

code	value
nd	nd

orgdiv3¶

code	value
nd	nd

orgdiv¶

code	value
nd	nd

ctdbid¶

code	value
CT	CT - Clinicaltrials.gov
ACTR	ACTR - Australian Clinical Trials Registry
ISRCTN	ISRCTN - International Standard Randomised Controlled Trial Number Register
NTR	NTR - Nederlands Trial Register
UMIN	UMIN - University Hospital Medical Information Network
ChiCTR	ChiCTR - Chinese Clinical Trial Register

doctype¶

code	value
au	audio
pr	press release
vi	video

deposid¶

code	value
1	Unicamp
2	Unifesp
3	Unesp
4	USP
5	ITA
6	UFSCar

ftype¶

code	value
audiogram	audiogram
cardiogram	cardiogram
cartoon	cartoon
chart	chart
chemical structure	chemical structure
dendrogram	dendrogram
diagram	diagram
drawing	drawing
exihibit	exihibit
graphic	graphic
illustration	illustration
map	map
medical image	medical image
other	other
photo	photo
photomicrograph	photomicrograph
plate	plate
polysomnogram	polysomnogram
schema	schema
workflow	workflow

lictype¶

code	value
open-access	open access
nd	not defined

pubtype¶

code	value
epub	electronic publication
ppub	print publication

hcomment¶

code	value
0	people can not comment
1	people can comment

license_text¶

code	value
BY	<a rel=”license” href=”http://creativecommons.org/licenses/by/3.0/”><img alt=”Creative Commons License” style=”border-width:0” src=”http://i.creativecommons.org/l/by/3.0/80x15.png” /></a> All the contents of this journal, except where otherwise noted, is licensed under a <a rel=”license” href=”http://creativecommons.org/licenses/by/3.0/”>Creative Commons Attribution License</a>
BY-NC	<a rel=”license” href=”http://creativecommons.org/licenses/by-nc/3.0/”><img alt=”Creative Commons License” style=”border-width:0” src=”http://i.creativecommons.org/l/by-nc/3.0/80x15.png” /></a> All the contents of this journal, except where otherwise noted, is licensed under a <a rel=”license” href=”http://creativecommons.org/licenses/by-nc/3.0/”>Creative Commons Attribution License</a>
nd	<p> </p>

ref-type¶

code	value
aff	Affiliation
app	Appendix
author-notes	Author notes
bibr	Bibliographic reference
boxed-text	Textbox or sidebar
chem	Chemical structure
contrib	Contributor
corresp	Corresponding author
disp-formula	Display formula
fig	Figure or group of figures
fn	Footnote
kwd	Keyword
list	List or list item
other	None of the items listed
plate	Plate
scheme	Scheme
sec	Section
statement	Statement
supplementary-material	Supplementary information
table	Table or group of tables

fntype¶

code	value
abbr	Abbreviations
com	Communicated-by information
con	Contributed-by information
conflict	Conflict of interest statements
corresp	Corresponding author information not identified separately, but merely footnoted
current-aff	Contributor’s current affiliation
deceased	Person has died since article was written
edited-by	Contributor has the role of an editor
equal	Contributed equally to the creation of the document
financial-disclosure	Statement of funding or denial of funds received in support of the research on which an article is based
on-leave	Contributor is on sabbatical or other leave of absence
other	Some footnote type, other than those enumerated.
participating-researchers	Contributor was a researcher for an article
present-address	Contributor’s current address
presented-at	Conference, colloquium, or other occasion at which this paper was presented
presented-by	Contributor who presented the material
previously-at	Contributor’s previous location or affiliation
study-group-members	Contributor was a member of the study group for the research
supplementary-material	Points to or describes supplementary material for the article
supported-by	Research upon which an article is based was supported by some entity

listtype¶

code	value
order	Ordered list. Prefix character is a number or a letter, depending on style
bullet	Unordered or bulleted list. Prefix character is a bullet, dash, or other symbol
alpha-lower	Ordered list. Prefix character is a lowercase alphabetical character
alpha-upper	Ordered list. Prefix character is an uppercase alphabetical character
roman-lower	Ordered list. Prefix character is a lowercase roman numeral
roman-upper	Ordered list. Prefix character is an uppercase roman numeral
simple	Simple or plain list (No prefix character before each item)

sec-type¶

code	value
cases	Cases/Case Reports
conclusions	Conclusions/Comment
discussion	Discussion/Interpretation
intro	Introduction/Synopsis
materials	Materials
methods	Methods/Methodology/Procedures
results	Results/Statement of Findings
subjects	Subjects/Participants/Patients
supplementary-material	Supplementary materials

Title Manager¶

Single-user program
Visual Basic
used in local server
Usage: to manage the databases: title, issue and section, it means, respectively the data of journals, their issues and sections of the table of contents.

Contents:

Opening the program¶

To open the program, use Windows menu, select SciELO, then Title Manager

Journal¶

Creating a new record¶

Select File-> Open-> Journals-> New.
Write the title of the journal and click on Open button.
Register the journal data. Read Journal form.
Click on Save button

Opening a record to edit the journal data¶

Select File-> Open-> Journals-> Open
Select the title you want to open
Register the journal data. Read Journal form.
Click on Save button

Deleting records of journals and their issues¶

It is used to remove records of one or more titles.

Use it only if you are sure the journal HAS NEVER BEEN PUBLISHED.

IT Is MANDATORY to keep all the titles registered, although ceased or removed off the collection, they must keep published.

If the journal has to be disabled, read Journal history.

It deletes the records of the databases title and issue locally. So, only after GeraPadrao, the title will be deleted from the website.

Select File-> Open-> Journals-> Delete
Select the titles to be removed.
Click on Remove button.

Journal form¶

ISSN¶

Field: 400

ISSN – print or electronic – which can not be changed because it is used as a key

Publication Title¶

Field: 100

Main title or title proper of the serial, in the language and form in which it appears.

Examples:

Publication title: British journal of surgery

Publication title: Journal of pediatrics

Publication title: Pediatrics (London)

Publication title: Pediatrics (New York)

Publication title: Abboterapia (English ed.)

Publication title: Abboterapia (Spanish ed.)

Subtitle¶

Field: 110

Publication Title: MMWR Subtitle: morbidity and mortality weekly report

Short Title¶

Field: 150

Enter the abbreviated title respecting the upper case letters, lower case letters and accentuation of the corresponding language, according to the standard.adopted by the journal

ISO Short Title¶

Field: 151

Enter the abbreviated title respecting the upper case letters, lower case letters and accentuation of the corresponding language, according to ISO standard 4-1984 and List of serial title word abbreviations. This field is mandatory for titles indexed in LILACS and/or MEDLINE. Examples:

Publication title: West Indian medical journal Abbreviated title: West Indian med. j.
Publication title: Abboterapia (English ed.) Abbreviated title: Abboterapia (Eng. ed.)
Publication title: Pediatrics (London) Abbreviated title: Pediatrics (London)

Section¶

Field: 130

Enter in this field the name of the Section, Part or Supplement, if exists, as it appears on the title page or its substitute, recording the first letter of the first word in upper case. Examples:

Publication Title: Acta ophtalmologica Title Section/Part: Supplement
Publication Title: Bulletin signaletique Section/Part: Section 330 Title Section/Part: Sciences pharmacologiques

Parallel Titles¶

Field: 230

Enter parallel titles in accordance with the sequence and typography in which they appear on the title page or its substitute, according to ISBD(S) rules. In case of more than one parallel title, enter them in the sequence which appears on the title page, separated by ENTER (one by lin - . Examples:

Publication Title: Archives of toxicology Parallel Title: Archiv fur Toxikologie
Publication Title: Arzneimittel Forschung Parallel Title: Drug research

Other Titles¶

Field: 240

Other forms of the title which appear in the serial such as: cover title which differs from the title on the title page, full title and other variant forms of the title. Include here lesser variants of the title proper which do not require a new record, but which justify their retrieval. In case of more than one title form, enter them in the sequence in which they appear, separated by ENTER (one by lin - Examples:

Publication Title: Obstetrics and Gynecology Clinics

of North America Other Forms of Title: Obstetrics and Gynecology Clinics
Publication Title: Journal of the National

Cancer Institute Other Forms of Title: JNCI: Journal of the National Cancer Institute

Old Title¶

Field: 610

Enter the preceding title, if there is one. If this title exists in the collection, in the journal homepage is presented a link from the current title to the preceding and vice-versa.

New Title¶

Field: 710

Enter the subsequent title of the serial. If this title belongs to the collection, in the site there will be a link between the title and its subsequent title, and vice versa.

Is Supplement¶

Field: 560

Link note: Note which acts as a link between the title of the supplement/insert and the main title or title proper. Enter the main title or title proper to which the supplement/insert is linked.

Has Supplement¶

Field: 550

Link note: Note which acts as a link between the main title or title proper and its supplements/inserts (titles generally published in separate form, with its own numbering, which complements the main titl - Enter in this field the title of the supplement/insert.

Registering the subject areas¶

Mission¶

Field: 901

Enter in this field the mission of the journal in English, Spanish and Portuguese. This is used in the home page of the journal. Examples:

Misión: To publish the results of original research which contribute significantly to knowledge in medical and biological sciences
Misión: La revista publica contribuciones originales de investigadores de todo el mundo en las áreas de parasitología, microbiología, medicina tropical, así como estudios básicos en bioquímica, inmunología, biología celular y molecular, fisiología, y genética relacionados con esas áreas

Subject/Descriptors¶

Field: 440

Descriptors; Standard terms used for the subject representation of the serial being described. Terms must be entered in capital letters. Cooperating Centers of BIREME System should use terms taken from DeCS (Descriptors in Health Scienc - . In case of more than one descriptor, enter them in sequence, separating them by ENTER, an item by line. Enter a maximum of 4 descriptors. Examples:

Descriptors: OCCUPATIONAL MEDICINE
Descriptors: PEDIATRICS
Descriptors: NEUROLOGY PEDIATRICS
Descriptors: GYNECOLOGY OBSTETRICS

Study Area¶

Field: 441

Select one or more subjects related to the journal. The site uses this content to presents the journal title in the site in the list by subject.

Indexing Coverage¶

Field: 450

Indexing Coverage – Enter in this field all the database in which the title is indexed. Each database in one line. Examples: - IM- Index Medicus - LL- LILACS - IL- Index Medicus Latino Americano - EM- Excerpta Medica - BA- Biological Abstracts - SP- LILACS-SP

Registering formal information¶

Initial Date¶

Field: 301

Enter the date of the first issue of the journal in ISO format (year in 4 digits, month 2 digits, day in 2 digits). Examples:

Initial date: Jan./Mar. 1974 19740100
Initial date: 1987 19870000
Initial date: Sept. 1988 19880900

Initial Volume¶

Field: 302

Enter the initial volume in arabic numerals. Omit this information for serials which do not include clear information on the volume. Examples:

Initial volume: 1
Initial volume: 4

Initial Number¶

Field: 303

Enter the initial number in arabic numerals. Examples:

Initial number: 1
Initial number: 2

Terminate Date¶

Field: 304

Date, in ISO format, in which the journal was published for the last time.Examples:

Termination date: 1984 19840000
Termination date: 1988 19880000

Final Volume¶

Field: 305

Number of the last published volume of the serial. Enter the final volume in arabic numerals. Examples:

Final volume: 10
Final volume: 12

Final Number¶

Field: 306

Enter the final number in arabic numerals. Examples:

Final number: 7
Final number: 10

Frequency¶

Field: 380

Code which identifies the intervals of time in which the issues of the serial are published.

Publication Status¶

Field: 50

Code which identifies if this title can be or already is published in the collection. In other words, if this title which can be processed by gerapadrao.

Current – title which can be accessed on the web site of the collection
Unknow – title which belongs to the collection, although it is not ready to be published Ceased – title which does not belong to the collection but it is related to title of the collection
Reports only – title which does not belong to the collection but it is used in reports

Alphabet¶

Field: 340

Enter data in this field the alphabet of the Original Title of the journal title.

Classification¶

Field: 430

Subject classification number assigned to the serial according to the classification system used by the Center.

Text Idiom¶

Field: 350

Languages in which the articles are published, including the translations. This field is related to the presentation of all the full texts of the site.

Abstract Idiom¶

Field: 360

Languages of the Abstracts

National Code¶

Field: 20

Code which identifies the title in the national system of serials of each country (or its equivalent) with the purpose of facilitating the transfer of data between this and other related systems. Enter in this field the code assigned by the institution responsible for the national system of serials of each country (or its equivalent). Examples:

National Code: 001060-X

(Code assigned by the Brazilian National Union List)
National Code: 00043/93

Standard¶

Field: 117

Standard used to the bibliographic references presentation. This content is related to the Markup program.

Controled Vocabulary¶

Field: 85

Enter in this field the controlled vocabulary used to the key words

Type of Literature¶

Field: 5

Type of literature

Treatment Level¶

Field: 6

Level of publication¶

Field: 330

SECS Code¶

Field: 37

Enter in this field the number assigned by BIREME which identifies the title in SeCS (Health Science Serials) database. Mandatory field for Cooperating Centers which input data to SeCS database. This field is used by the system to generate the holding files which are to be transfered to SeCS database. This field must be entered if SECS is recorded in Field 040; Related Systems. Examples:

SECS Number: 2
SECS Number: 4

MEDLINE Code¶

Field: 420

MEDLINE Code (Journal Cod - of the title when it is indexed in MEDLINE databases.

MEDLINE Short Title¶

Field: 421

Short title for MEDLINE

Registering license or copyright¶

Text provided by Creative Commons site according to the license choice¶

Field: 540tl

Enter in HTML in English, Portuguese, Spanish, a text, which inform the license to use the content of the journal (Creative Commons).

Copyrighter¶

Field: 62

Copyrighter Examples: - Brazilian Journal of Medical and Biological Research - Sociedade Brasileira de Genética - Instituto Universitário de Pesquisas do Rio de Janeiro - Revista Brasileira de Ciências Sociais

Registering the history of journal’s status in the collection¶

Journal history¶

Field: 51abcd

Date and status which identify the changes of the journal’s status in the collection. Date must be in ISO format YYYYMMDD Status can be:

Ceased (D): journal will not be published any more.

Current (C): journal published currently.

Suspended (S):journal is no longer according to collection´s criteria. In the future it can become current.

Journal’s status history in this collection¶

Field: 51

Repetitive.

subfield a: initial date, ISO format

subfield b: status which value is C

subfield c: final date, ISO format

subfield d: status which value is D or S

Registering data for the website¶

Acronym (Lowercase and/or Uppercase letters)¶

Field: 930

Enter in this field the acronym of the journal, max 8 characters length, in capital letter or not. It must be unique comparing to the other titles. It is used for the name of the folder in which are saved all the files related to the journal (markup, body, images, et - and also used for the prefix to the sections code of the journal.

Acronym¶

Field: 68

Name of the folder which contains the files of the journals and which is in serial folder. It is automatically filled as filling in the field acronym of the title of the journal

ISSN Type¶

Field: 35

Identifies the type of the CURRENT ISSN.

Current ISSN¶

Field: 935

Enter the current ISSN. It can be different or equal to the ISSN used as ID, but it is usually the online ISSN.

URL of the main collection¶

Field: 690

Enter the URL of the main collection site. If the journal is published in SciELO Brazil, then www.scielo.br

URL of Submission Online¶

Field: 692

Enter the URL of the submission site

URL of the journal¶

Field: 69

If the journal is published in another site, enter in this field the other site location

FTP¶

Field: 66

Enter in this field the information about PDF files of the articles. not available – PDF unavailables art (article base - – one PDF file for each article iss (issue base - – one PDF file for one issue

User Subscription¶

Field: 67

Identifies how to access to the articles by subscription. Select the corresponding option: - sub ; regular subscription - reg; electronic registration - na; not available, no hay subscription

SciELO Net¶

Field: 691

Select the collections to which the journal belong.

Registering the record data¶

Notes¶

Field: 900

Enter in this field, in free style, all information of interest to the Center about the serial.

Center Code¶

Field: 10

Code which identifies the center responsible for the creation of the bibliographic records

Identification Number¶

Field: 30

Sequential number assigned and controlled by the Cooperating Center which identifies the serial in the database. Enter in this field the number corresponding to the title being described. This field is used in the system in order to link the title record with its corresponding issues, therefore being mandatory. Examples:

Record identification: 1050
Record identification: 415

Creation Date¶

Field: 940

Automatically filled with the date of the registration.

Documentalist (Creation)¶

Field: 950

Initials of the responsible for the register creation.

Update Date¶

Field: 941

Automatically filled with the updating date.

Documentalist (Update)¶

Field: 951

Initials of the responsible for the register updating.

Sections¶

It manages all the sections of the table of contents of the all the journal issues.

Opening the journal sections form¶

Select File-> Open-> Sections
Select a title and click on Open button

Sections form¶

As opening the form, it will be presented a screen with four columns:

Seccode (code sections)

titles of the section in Spanish

titles of the section in Portuguese

titles of the section in English

The code of sections are formed by the Journal acronym, followed by 010, or 020, or 030, and, so on.

The title of the sections may or not be in all the languages of the interface.

Fig 1a - List of sections of the journal

The list can be rearranged, by clicking on any column. For example, clicking on code column, the list will be sorted by code.

Fig 1b - List of sections, ordered by the English column

Creating a section¶

1. Register the section code according to the acronym format, followed by 010, or 020, or 030, and successively.

Figure 2 - Field to enter the section code

Register the fields for section title

Figure 3 - Fields to enter the section titles
Click on Insert button
Click on Save button

NOTES:

Only after clicking on the Save button, the record will be up to date with all the changes.

Editing the section¶

Click on the line of the section to edit. Code and section titles go to the fields.

Figure 4 - selected section to edit or delete
Edit the section titles
Click on Insert button

Figure 5 - Insert button
Click on Save button

NOTES:
Only after clicking on the Save button, the record will be up to date with all the changes.
It is allowed to change only the sections which are not in use.

Deleting a section¶

Click on the line of the section to be deleted. Section code and titles will go to their fields.

Figure 6 - selected section to edit or delete
Click on Remove button

Figure 7 - Remove button
Click on Save button

NOTES:

Only after clicking on the Save button, the record will be up to date with all the changes.

It is allowed to change only the sections which are not in use.

Figure 8 - Buttons: Save, Close, Help

Section database¶

ISIS Base. A record by title. Each record contains the following tags:

tag
035	ISSN. Corresponds to the field of 400 of TITLE
048 subfield l	Language of table of contents’ header
048 subfield h	title for table of contents’ header (Table of contents (en), Sumario (pt), Tabla de Contenido (es))
049 subfield c	code of the section
049 subfield l	language of the section
049 subfield t	title of the section
091	Date ISO to register the update date
100	Journal’s title. Corresponds to the same field of TITLE.
930	Journal’s acronym in uppercase

Issues¶

Opening the program¶

Select File-> Open-> Issues
Select a title and click on Open button

Important concepts¶

Read:

Issues form¶

From this screen, you have the following options:

List the issues
Create an issue
Edit an issue
Delete an issue

Listing issues¶

Clicking on the

button to list all the issues.

If you want to list all the numbers of a given volume, fill the volume field, then click on the

button.

The first highlighted line in orange is one example of ahead numbers of the year 2009.

The second highlighted line in blue is an example of a regular number.

The third highlighted line in purple is an example of press release number of v43n5 (blue).

The fourth line highlighted in red is an example of number press release ahead to 2009 (orange).

The lines highlighted in green are examples of supplement of volume.

The lines are highlighted examples of numbers review / provisional.

Identifying the issue and its sequential number¶

To create, edit or remove, identify the issue, filling the volume, issue, supplement, complement, sequential number. Read about it.

Issue identification¶

label	field
volume	31
supplement of volume	131
number	32
supplement of number	132
complement	41
sequential number	36	The sequential number is the year followed by the order for publication of the issue within a year. The sequential number is part of the PID of the issue. Must not be modified after publication of the issue. It also is used for the presentation of issues on the page all the issues, giving their order of presentation in the table.

Identifying regular issues¶

Fill the volume and number.

The sequential number is the year followed by the order of the issue within a year. Eg: 20101 (first issue within a year).

Identifying supplements¶

When they exist, fill volume, supplement of volume (when there is no number), number, and supplement of number.

If the supplement is identified only with the word Supplement, fill in with 0, otherwise the label which identifies the supplement, for example, 1, A, etc.

On the site, so that all supplements are presented after the regular issues within a year, the sequential numbers of the supplements must be greater than the sequential number of the last regular issue. Eg: If there are 4 regular numbers in the year, then the sequential number for the supplements starts in 5.

Identifying ahead or review / provisional issues¶

Fill in the number field the word ahead, for ahead issue. By convention its sequential number is 50. Fill in the number field the word review, for review or provisional issue. By convention its sequential number is 75.

The sequential number is the year followed by the order of the issue within year, but by convention:

Ahead is equal to 50
Review / provisional is equal to 75

Indentifying press release issues¶

Populate the same fields in accordance with the rules above, plus pr in the complement. The sequential number is the year followed by the order of the issue within a year, but by convention starts in 100.

Problems on filling the sequential number¶

When the sequential number and the issue identification do not match, the program presents two conflict situations:

Sequential number belonging to another issue¶

When the user informs a sequential belonging to another issue, the program does not open the issue data, and informs the sequential number belongs to another issue.

It is also possible that the user have misinformed the issue identification and not the sequential number. The user is responsible for checking and correcting the data filled in before proceeding.

Mistake or replacement?¶

When the user reports an issue identification and a sequential number which do not match and the sequential number DOES NOT BELONG TO another issue, the program allows to:

open the issue, using the identification informed, but correcting its sequential number
change the issue’s sequential number to the informed one

Warning

The sequential number is part of the PID, so it must not be changed if the issue is already published on the site. The program allows the change of sequence number, if it does not belong to any other issue. The program does not know if the issue is already published or not. The user must be responsible for knowing it.

Creating/editing an issue¶

Identify the issue. Read Issue identification.
Click on the Open button

General data¶

Status¶

Field: 42

Status of the issue. It indicates if the issue would be available on the website.

Number of documents¶

Field: 122

Number of documents (articles and texts) of the issue. Converter checks this value with the amount of files in the folder serial/<acronimo>/<issueid>/markup.

Date ISO¶

Field: 65

Date of publication of the issue in ISO format (YYYYMMDD) = 4 digit year, followed by two digits for month, 2 digits for day, with possible 00 if the day is not important.

This date is used to generate the bibliographic strip (next screen) and it is also used by Converter to check the date.

Issue’s title¶

Field: 33

This field must be filled, if there is/are the issue’s title. Thematic or special issues usually have it.

Cover¶

Field: 97

Part¶

Field: 34 Into disuse.

ISSUE ISSN¶

Field: 35

Fill it with the ISSN used by the journal at the time this issue was published.

Editor issue¶

Field: 62

This field must be filled, if there is/are the issue’s editor.

Standard¶

Field: 117

Standard used by the journal.

Markup done¶

Field: 200

It indicates whether the Markup of this issue has already been done. If so, the issue will not be listed on Markup program.

Controlled Vocabulary¶

Field: 85

Controlled vocabulary used by the journal.

Bibliographic strip¶

Field 43, one occurrence for each language (es, en, pt).

Subfield l: possible values: es (for Spanish), pt (for Portuguese) or en (for English)
Subfield t: abbreviated title, value from the Title/Field 150.
Subfield v: volume
Subfield w: Supplement of Volume
Subfield n: number
Subfield s: Supplement of number
subfield c: publisher location
Subfield m: month of publication, generated automatically by the ISO date provided in the previous screen, however, editable
Subfield y: year of publication, automatically generated by the ISO date provided in the previous screen. This value is checked against ISO date.

Table of contents¶

On this screen, the table of contents.

The user must choose the sections that are part of the issue.

The program will present the table below, sorted by language.

If there are missing sections, the user must click on Create sections which open a screen for the Sections’ form.

Header of table of contents¶

Field: 48, one occurrence for each language (es, pt, en).

Subfield l: language header. pt (Portuguese), es (Spanish), en (English)

Subfield h: header. Sumario (en), Tabla de contenido (es), Table of Contents (en)

Sections Data¶

Field: 49

Subfield l: language of the section pt (Portuguese), es (Spanish), en (English)

Subfield c: section code/id, formed by acronym, followed by 010, or 020, or 030, and so on

Subfield t: section title

Creative Commons License¶

Text provided by the Creative Commons site in accordance with the choice of license

Field: 540, for each language an occurrence (es, en, pt).

Subfield l: language of the license text (pt (Portuguese), es (Spanish), en (English))
Subfield t: license text in HTML format

Deleting issue¶

1. Informing the issue and its sequential number 1. Click on Remove button

NOTE: This option only delete the record of the issue database, does not remove the issue from the website.

Issue database¶

ISIS Base. One record per issue. Each record contains the following tags:


030		Short Title. Corresponds to 150 of TITLE
031		Volume
032		Number
033		Title of the issue
034		Party
035		ISSN. Corresponds to the field of 400 TITLE
036		Seq Num
041		Complement. Identify a press release number\|\|
042		Status
043		Legend
043	v	volume
043	w	Supplement volume
043	n	number
043	s	Supplement number
043	y	Year
043	c	City
043	m	last
048	l	Language header summary
048	h	Header Summary (Table of contents, summary, etc.)
049	c	Code sections
049	l	Language Sections
049	t	Title of the sections
062		Editor of the issue
064		Date of publication. for the year (four digits), m month (two digits)
065		Date ISO
085		Controlled Vocabulary
091		Date ISO to register the update date\|\|
097		Cover
117		Standard (vancouver, ISO, ABNT, etc.)
122		Number of documents
130		Title of the journal. Corresponds to the field of 100 of TITLE database\|\|
131		SuplVol
132		SuplNum
140		Sponsor
200		Markup done
230		corresponds to the same field of TITLE database
540		Text provided by the Creative Commons site in accordance with the choice of license
700		position of the record on the basis of an issue. Value equal to 0, first record
701		Counter record type. Value of 1
706		type / name of the record. Value of i (of issue)
930		Journal’s acronym in uppercase
935		ISSN of the journal at the time the issue had been published. Corresponds to the field of 935 TITLE

Converter¶

single-user program built in Visual Basic, to use only by a centralized server, denominated local server. It is mandatory only one installation by SciELO collection or instance.
Converter reads the files from markup and body folders, and the databases in title and issue folders, then generates a ISIS database in base folder of the corresponding journal issue.

Opening the program¶

Checking the program version¶

To check the version of the program, see How to check the program version.

Changing the language of the program¶

To change the language of the program’s interface, see Change the language of the program.

Running the program¶

Select Files.
Fill the fields:
- journal’s title: select the title of the journal.
- year: FILL ONLY if it is AHEAD or REVIEW number
- volume: fill it in with the volume
- supplement of volume: fill it in with the supplement of volume, if it exists
- number: fill it in with the number. If it is an ahead or review/provisional number, use ahead or review, respectively
- supplement of number: fill it in with the supplement of number, if it exists
- part: fill it in, if it exists. Recently it is used to press release, fill it in with pr.

Click on OK button.
Converter uses these data to identify the issue’s, markup and body folders. If the data are correct, the program will list the markup files.
Click on Convert button.
Converter will convert the selected files.
For each file, the program:
extracts the marked data

compares the issue’s data in the markup file and in the issue database, managed by Title Manager->Issues.
If there is some conflicting data, the data are not converted to the database. It is a fatal error. The user must check and correct the data in the markup document (using Markup program) and/or in issue database (using Title Manager).

If the issue’s data is correct, the files are converted to the database and the result will be shown on the screen.

Results:
successfully converted: [], in red.

converted, with errors: [X], in blue before its name. They have some markup errors, but not fatal enough to avoid conversion. For example, markup error, probably identified by Parser, but not corrected by the user.

not converted: at the inferior part, in green. It is usually related to issue’s data, such as ISSN, abbreviated title, volume and number, which do not match in the markup file and in the issue database.
Clicking on each file in the result area and then on Result button, the user can see how the conversion run.

Successfully converted

Converted, but no fatal error: markup error

Converted, but no fatal error: some bibliographic references not identified

Converter locates each bibliographic reference of the markup file in the body file, identifying the points where [Links] must be inserted at the article page, in the website.

Clicking on [Links], a window is open to display a list of links to the referenced fulltext.

If there are bibliographic reference location errors, Converter will present the result bellow:

Not converted, because of fatal errors

XML SciELO¶

DOS Batch program
local server

This program generates XML and SGML files to PubMed and ISI.

For PubMed, there are two types of files:

Journal data:

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinkout.section.files.Resource_File#files.Resource_File_Format. Sent once or every time the journal data was changed.
Articles data:

http://www.ncbi.nlm.nih.gov/entrez/query/static/spec.html Sent one XML file for each issue.

Installation¶

This program is installed in PROGRAMS_PATH on the local Server using the SciELO PC-Programs package, where PROGRAMS_PATH is the path for all the SciELO PC programs.

The examples are considering PROGRAMS_PATH equal to c:\scielo.

It is also necessary to install java, if there is no java installed.

Configuration¶

Configuring the files and paths¶

Some configurations are done automatically as installing the PC Programs. The configuration files for all the PC Programs is c:\scielo\bin\scielo_paths.ini.

This program use the following parameters of this configuration file:

; Serial Serial Directory=f:\serial\,required … ; xml_scielo XML_SCIELO_PROGRAM_PATH=c:\scielo\xml_scielo PHP_EXE=c:\server\php\php.exe JAVA_EXE=java PubMed_DIR_COPY=c:\scielo\serialSCI_LISTA_SITE=c:\scielo\web\proc\scilista.lst PubMed_PROVIDER_ID=3081

Serial Directory: it is the place for all the journal and issues data. So, it indicates to the program where to find the data: c:\scielo\serial\title\title, c:\scielo\serial\<revistas>\<issue>.
XML_SCIELO_PROGRAM_PATH: it indicates the place where the programs is installed. E.g.: c:\scielo\xml_scielo.
PHP_EXE: it indicates the full path to php.exe, used for XML transformation. E.g: c:\server\php\php.exe.
JAVA_EXE: it indicates the full path to java or just java, if it is already in the PATH, used for XML transformation. E.g: java.
PubMed_DIR_COPY: it indicates the place where there Will be a copy of the generated files.
SCI_LISTA_SITE: it indicates the list used to generate the website. This program uses this list to create another list, used by itself.
PubMed_PROVIDER_ID: it is the ID of the provider. SciELO is one of the providers whose ID is 3081, for all the SciELO Collection.

Configuration of the data¶

If it is the first installation, you have some procedures to execute.

There is a file in c:\scielo\xml_scielo\config.example. You have to copy and rename to config.

Configure the files:

PubMed\doi_conf.txt
PubMed\config\config.seq
PubMed\journals\journals.seq

File doi_conf.txt¶

It contains the data of the Publisher and the prefix given by CrossRef, according to the agreement signed by CrossRef and the SciELO of each country. IF YOUR SCIELO DOES NOT HAVE IT. SO THIS FILE MUST BE EMPTY.

INSTITUTION SPACE E-MAIL SPACE PREFIX

File config\config.seq¶

The file configconfig.seq is to informe to the program which articles or text should not be sent to PubMed, because some kind of documents are not accepted. So by their section in the table of contents it is possible to know if the document would be accept or not. So, this file contains the list of sections whose documents will not be accepted by PubMed.

Acronym space sectionId

File journals\journals.seq¶

This file journals\journals.seq contains data used to generate XML file of the journal: journals_acronimo.xml. This is the first XML file which must be sent to PubMed in order to register the journal. Read more: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinkout.section.files.Resource_File#files.Resource_File_Format.

Its format is:

ACRONYM SPACE FIRST_YEAR_IN_PubMed SPACE SCIELO_URL SPACE ISSN

One line for each journal.

Executing¶

It has to be executed using the command line in DOS.

Go to the folder where this program is installed. E.g.: c:\scielo\xml_scielo\proc.

In proc you will find three scripts:

GenerateXML_all.bat: generates at the same time ISI and PubMed
GenerateXML_ISI.bat: generates SGML to ISI
GenerateXML_PubMed.bat: generates XML to PubMed

Provide a list similar to scilist, to execute any of them.

The program will open the scilist file and you have to check it, and include or remove lines, according to what you want to generate.

To generate also the XML file which contains journal data, journals_<acronimo>.xml, add one more parameter “YES”:

hcsm v13n2 YES

To generate ONLY the XML file which contains journal data, journals_<acronimo>.xml, the second parameter must be “NONE” and third one must be YES.

hcsm NONE YES

Programs for Markup computers¶

Markup¶

single-user program, built in Visual Basic Application for Word, to descentralized use in any workstation.
Its installation can be done in several computers, others than local server.
tool to identify bibliographic elements in the articles and texts, according to SciELO DTD for article and for text, based on standard ISO 8879-1986 (SGML - Standard Generalized Markup Language) and ISO 12083-1994 (Electronic Manuscript Preparation and Markup).

With this program, the user can:

open the articles or text files
identify the bibliographic elements in the file, by select them with the mouse or keyboard and then tagging them, according DTD
markup bibliographics references semiautomatically
validate the identification according to article dtd.html#article and for text
generate PMC XML (under development) http://dtd.nlm.nih.gov/publishing/3.0/. Read the instructions given by Markup PMC.
validate PMC XML
preview the text generated from XML PMC

Before using the Markup¶

you must have one article or text by file
check if the file contents is same of printed version or PDF file
check if the file format is HTML, .doc, .rtf
check if the number which the articles belong is recorded in title and issue databases
If the markup will be done in a different machine than local server, copy the files bellow from (local server)binmarkup :
- ??_issue.mds - it is updated when a new issue data is input on or modified in the database
- issue.mds - it is updated when a new issue data is input on or modified in the database
- ??_attb.mds - it is updated when a new code table data is input on or modified in the database
- automata.mds - it is updated when a new title data is input on or modified in the database
- journal-standard.txt - it is updated when a new issue data is input on or modified in the database

Open the program¶

Go to the menu, select SciELO and Markup

The program will try to open the Microsoft Word Program which is set in the file bin\markup\start.mds.

If the path is not valid, the program will ask for the right path of Microsoft Word Program.

Other option is to change this path by editing the bin\markup\start.mds file.

Just in case it doesn’t appear the message about macro execution, you need to drop the macro’s security level down.

In Word 2003, it appears as following:

If Word program opens correctly, the Markup bar will appear at the inferior part of the screen.

In Word 2007, it is different. The Markup bar will appear inside the Supplement group.

Open an article or a text file.

As clicking on Markup button, two options will be shown: configuration and Markup DTD-SciELO.

In Word 2007:

If the macro was not loaded normally, the message bellow will appear:

To solve it, select the Tools->Supplements and Models option of the menu.

So, remove the incorrect item, and put on the right path file corresponding of c:\scielo\bin\markup\markup.prg.

Using the program¶

Open a .html or .doc file.

Click on Markup DTD-SciELO to start the markup.

The Word bars will disappear, remaining only the Markup bars:

white: files operations, edit or eraser a tag, automatic markup
orange: floating tags, can be used in any document part
green: tags that have a specific hierarchy of DTD

In Word 2007, all these tags bars are agrouped in Supplements.

The markup starts when you click on document type button:

Article: specifies scientific articles. They must have key-words, abstracts and bibliographic references. It is accounted in bibliometric module as scientific production.
Text: specifies texts that are part of a journal, but don’t have scientific worth. Ex.: Editorial, interview, review, etc.

The bars¶

General bar¶

Exit button¶

To exit the program, click on Exit button.

Choose one of the options bellow.

Element’s attribute edition button¶

To edit attributes of an element, select the name element, then click on the edit (pencil) button. The program will ask for changing the values of the attributes.

Delete element button¶

To delete one element and its attributes, select the element name, then click on the delete button. The program will ask to confirm this action.

Save file button¶

To save a file, click on the save button.

Automata 1 button¶

To mark bibliographic references automatically:

the journal have to have an Automata file (read how to programming an automata), which configures the rules to identify the references elements.
select one bibliographic reference until its final dot, including, and then click on the Automata 1 button.

This action will activate a tool which will try to identify the bibliographic reference elements automatically. The tool will present the several possibilities of identification. So the user have to select the correct one.

Automata 2 Button¶

To mark a set of bibliographical references automatically (available only for Vancouver standard). Select one or more bibliographic references and then click on the Automata 2 button.

The program will mark all references it can identify and will also keep the original reference, marked as [text-ref]. Thus the user can compare them in order to check if the reference was correctly identified and proceed the correction, if it is necessary.

Validate markup button¶

To validate the markup, click on the Validate markup button. It will run the SGML Parser.

Floating tag bar¶

The floating elements are the ones which can appear in any part of the text.

aff: identifies an author affiliation
ign: identifies a text which can be ignored
tabwrap: (only valid for XML PMC)
figgrps: (only valid for XML PMC)
figgrp: (only valid for XML PMC)
equation: (only valid for XML PMC)
cltrial: identifies clinical trials data
list: (only valid for XML PMC)
xref: (only valid for XML PMC)
uri: (only valid for XML PMC)
sciname: (only valid for XML PMC)

Hierarchical tags bar¶

This bar groups the elements according to the DTD. This bar will present the elements of one hierarchical level each time. As the user goes to a down or up level, the bar presents respectively, only the down or up level. The user goes to a down level, when clicks on an element or on a down arrow, and goes to an up level, clicking on the up arrow.

If there is no element marked in the text, then the initial elements buttons (article and text) are presented.

If there are any element marked in the text, the level just below the article or text are presented.

Navegation¶

The down and up arrows are to navegate between hierachical elements levels. The user should find the elements to mark in the bars.

Clicking on the down arrow next to bibcom, its children (hierarchical related) will appear.

Clicking on the up arrow, at the right side of the bar, the elements of the superior level will appear.

For example:

Down¶

Bar of front element

Bar of front element’s children

Bar of titlegrp element’s chidren

Up¶

Error messages¶

To avoid errors and to guide the user during the markup, the program presents some messages in case the procedures described previously have not been correctly done. For example:

If the user has clicked on an element button and no text was selected.
If a mandatory atribute value wasn’t filled in.
If the user try to insert a tag in an incorrect place, disaccording to DTD.

Bad value to a mandatory attribute

The user tried to identify an element which is not according to the hierarchical structure / DTD

the user has clicked on an element button and no text was selected

Markup PMC¶

Use the same Markup Program. So, read its documentation.

And use a copy of the markup file to generate the XML file to PMC.

The PMC Markup will be done on a copy of a markup file.

PMC Files Specifications: http://www.ncbi.nlm.nih.gov/pmc/pub/filespec/

The bars¶

General bar¶

Generate XML file button¶

To generate the XML files to PMC, the user must guarantee that xmlbody and other tags must exist, including the regular markup.

Validate XML file button¶

Click on it, to validate the XML file.

If the XML file is invalid:

If the XML file is valid:

Preview the text generated using the XML file button¶

To preview the text, generated from XML file, in order to check if how the fulltext will be presented in the website, click on the Preview text button.

Markup button¶

To go back to markup file.

Floating tag bar¶

The floating elements are the ones which can appear in any part of the text.

aff: identifies an author affiliation
ign: identifies a text which can be ignored
tabwrap: identifies a table (includes label, caption and image) (only valid for XML PMC)
figgrps: identifies a compound figure (Fig 1A, 1B, etc), and each one must be figgrp (only valid for XML PMC)
figgrp: identifies a figure (includes label, caption and image) (only valid for XML PMC)
equation: identifies an equation (represented by image or LaTex or mml:math) (only valid for XML PMC)
list: identifies a list (only valid for XML PMC)
xref: identifies cross reference (only valid for XML PMC)
uri: identifies external links (only valid for XML PMC)
sciname: identifies scientific names (only valid for XML PMC)

SGML Parser¶

single-user program built in Visual Basic and C, and uses sp120.dll library.
It is always installed, because it is used in several situations: by the Markup, by the Converter (internally), and stand-alone.
tool to check whether the markup done using Markup is according to DTD SciELO.

This program can be run:

or from Markup
or by PC Programs’ menu
or by Converter, internal use, to analyze and obtain the values of the elements and their attributes.

Parser called by Markup: the file, which is open in the Markup program, is open in SGML Parser program.

Parser called by Menu: after opening SGML Parser program, the user have to open a file .txt or .sci, by accessing the File menu option.

This procedure must be done to *.sci files generated by Converter when some problem is identified in the marked files.

Configuration¶

Access the Menu and select Configuration option.

The options Add ignore markup to document and Add SGML declaration to document must be selected, when the document is:

an article
- File Containing the DTD = C:\SCIELO\BIN\SGMLPARS\article4_0.dtd
- Document Type Name = article
a text
- File Containing the DTD = C:\SCIELO\BIN\SGMLPARS\text4_0.dtd
- Document Type Name = text

Document analysis¶

After configuring, the user have to use Parse menu option in order to analyze the marked document.

If everything is correct, the message bellow is presented:

So, the user can exit the program.

If there are errors, the Parser will indicate the line and the error type occured. In this case, the user must go back to Markup program and make corrections and then repete the procedure of using SGML Parser, until there is no error.

Support¶

How to get support

Welcome to SciELO PC Programs’ documentation!¶

Download¶

Requirements¶

How to install¶

Programs for local server¶

Programs for Markup Computer¶

Concepts of the SciELO Methodology¶

Local server¶

SciELO collection or instance¶

Types of issues¶

Sequential number¶

Folders Structure¶

Programs folder¶

Data folder¶

Journal’s folder¶

Issue folder¶

Local website¶

Programs for local server¶

Code Manager¶

Opening the program¶

Managing the tables¶

Accessing a table¶

Removing a row of the table¶

Updating a row of the table¶

Creating a new row¶

Technical information¶

Code database¶

NewCode database¶

Code database Content¶

doctopic¶

role¶

standard¶

ccode¶

literature type¶

treatment level¶

status¶

month¶

date¶

country¶

publication level¶

alphabet of title¶

language¶

frequency¶

indexing coverage¶

acquisition priority¶

state¶

article status¶

stitle¶

illustrative material type¶

version¶

from¶

to¶

keyword priority level¶

toccode¶

scheme¶

ftp¶

usersubscription¶

id¶

stud area¶

rid¶

dateiso¶

count¶

pii¶

pages¶

issue status¶

idiom interface¶

table of contents¶

sponsor¶

orgname¶

no¶

scielonet¶

issn type¶

orgdiv1¶

orgdiv2¶

orgdiv3¶

orgdiv¶

ctdbid¶

doctype¶

deposid¶

ftype¶