[Isis-users] Import RIS Files using MX

Sat Mar 10 19:25:10 CET 2018

Ok, as Egbert says, conversion of records is not a task for scary people 
with a weak heart
First of all you have to know the format in which the data is received 
and to know better the format to which you want to convert it.
In the present challenge of our colleague Adagilson of the prestigious 
institution Fiocruz of Brazil, he wants to convert records in .ris 
format (probably from Scopus) into LILACS format of Bireme.

Well, let's give some ideas, but a detailed work comes at the level of 
consulting. But if you have faith, and are stubborn enough you will 
achieve it (do not look at me) :-)

Let's start with an example file with four records exported from Scopus 
in RIS format.
This file if you open it with notepad surely will appear with all the 
lines continous without a line break and in UTF chars.
To insert the line breaks (if you work in Windows) you should open it 
with Wordpad and then save it. This makes the miracle.
The example file is in the attachment: export.ris (already prepared for 
Windows)

Then run the followin script (one line at a time, first)

*mx seq=export.ris lw=8000 pft=v1/ now tell=100 > xxx0.txt
mx seq=xxx0.txt lw=8000 create=xxx1 now -all tell=100
mx xxx1 "proc=if v1*0.10:'  - ' then else 'd.' fi" copy=xxx1 now -all 
tell=100
mx xxx1 iso=xxx1.iso now -all tell=100
mx iso=xxx1.iso create=xxx2 now -all tell=100

:: gris is a gizmo file prepared to convert RIS into LILACS
:: the gizmo is part of the attachment
mx xxx2 gizmo=gris pft=v1/ lw=8000 now  tell=100 >> xxx2.txt

:: Open the file xxx2.txt and add as the first line: !ID000000  
(required by id2i.exe )
:: and delete the very last line of the file
id2i xxx2.txt create=xxx3
mx xxx3 gizmo=gutf8ans create=xxx4 now -all tell=100

it is recommended also   mxcp xxx4 create=xxx5 clean tell=100
*
Well, now comes the "detailed conversion" part or tuning
For example, the descriptor field v87 must have ^d at the beginning, the 
pages in v14 have ^ fnn ^ lnn etc
This is done with specific procs of LILACS

But, what if one wants to convert the source file to another format, for 
example CEPAL or MARC, etc?
How do we know the tags that the RIS format uses (or any other that we 
use as input?)
That is, how do we prepare a tailor-made gizmo GRIS?
In order to do that we have to scan the tags used in the source file

This is the way to do
Take the intermediate file xxx2
*mx xxx2 "proc='Gsplit/clean=1=-'"  "fst=1 0 v1[1]" fullinv=xxx2 tell=100
ifkeys xxx2   > tags.txt*
this will report all the tags present in the source file
Now you have to prepare a table like the following

*A2 *

*!v010!*

*Author (other)*

*AB *

*!v083!*

*abstract*

*AD *

*!v110!*

*affiliation*

*AU *

*!v010!*

*author*

*CY *

*!v056!*

*City of the meeting*

*EP *

*!v015!*

*end page*

*ER *

*!ID000000*

*end of record*

*IS *

*!v032!*

*issue*

*JA*

*!v130!*

*Abridged title*

*JF *

*!v030!*

*Journal*

*KW *

*!v087!*

*Keyword*

*N1 *

*!v061!*

*Notes*

*PB *

*!v062!*

*editorial*

*PY *

*!v064!*

*publication year*

*SN*

*!v035!*

*ISSN*

*SP *

*!v014!*

*starting page*

*T1 *

*!v012!*

*title*

*T2 *

*!v013!*

*titulo idioma original*

*T3 *

*!v053!*

*publicacion de la conferencia*

*TY *

*!v005!*

*Record type*

*UR *

*!v008!*

*url*

*VL *

*!v031!*

*volumen*

*Y2 *

*!v054!*

*Date of meeting*

*LA*

*¡040!*

*language*

OK people, enjoy it

Regards
Ernesto Spinak

El 10/03/2018 a las 8:42, De Smet Egbert escribió:
> Yes, this is the same idea, only using mx with gizmo to create the tag-replacements. That is for real ISIS-aficionados like Ernesto : 'ISIS for always and for all (purposes/people) "...
> But the nice thing about his solution - contrary to mine - is that you can put it in a script of mx-commands (and finally the retag command) and therefore run at any time with just the script launching command. If the conversion has to be done regularly that is a clear advantage.
>
> Egbert de Smet
> Universiteit Antwerpen
> ________________________________________
> From: Piet De Keyser <piet.dekeyser at ucll.be>
> Sent: Friday, March 9, 2018 11:38 PM
> To: De Smet Egbert; Adagilson Batista Bispo da Silva; 'isis-users'
> Subject: Re: Import RIS Files using MX
>
> Dear colleague,
>
> Let me quote here from a mail put on this list by Ernesto Spinak in January 2017, where he explains how to convert tagged files into an ISIS database using MX. It seems rather complex at first fight, but I can asure you it works fine.
>
> Piet de Keyser
> Belgium
>
> Text from here was by Ernesto Spinak:
>
> Process
> Create a gizmo with all labels declared in your source file
> in this case, we prepared a text (take care of spaces) to create a gizmo named glabel
> NMN |!v001!
> DES: |!v002!
> DIM: |!v003!
> DOBN: |!v004!
> DON: |!v005!
> LOC: |!v006!
> 1) mx seq=labels.txt create=glabel now
>
> 2) read the source file into a database
>     mx seq=CCH2.txt lw=8000 create=xxx now -all tell=100
>
> 3) mxcp xxx create=xxx1 clean   (get rid of extra spaeces and garbage)
>
> 4) create an ID text with cisis labels
> mx xxx1 gizmo=glabel "pft=if s(v1):'!v001!' then '!ID 000000'/ v1 else v1 fi/" lw=8000 now > xxx2.txt
>
> 5) ID2I xxx2.txt create=final
>
> 6) retag your final mst
>
> Result
> mfn=     1
>    1  «J 2»
>    2  «Insignia (cockade) worn by member of German Schutztruppe; round rosette-shaped; red, white, black»
>    5  «Mr Borg, 1956»
>    6  «Alte Feste, Store Room»
> ..
> mfn=     2
>    1  «J 5 (a, b)»
>    2  «Medals û Herero-Land, Gross-Namaland»
>    5  «Sergeant-Major A. Bok, 1956»
>    6  «Alte Feste, Store Room»
> ..
> mfn=     3
>    1  «J 6 (a, b)»
>    2  «Medals 1904-1908, 1914-1918»
>    5  «Sergeant-Major A. Bok, 1956»
>    6  «Alte Feste, Store Room»
>
>
> applause, drums and horns!!!!
>
> Enjoy it
> Ernesto Spinak
> ________________________________________
> Van: isis-users <isis-users-bounces+piet.dekeyser=ucll.be at iccisis.org> namens De Smet Egbert <egbert.desmet at uantwerpen.be>
> Verzonden: vrijdag 9 maart 2018 22:24
> Aan: Adagilson Batista Bispo da Silva; 'isis-users'
> Onderwerp: Re: [Isis-users] Import RIS Files using MX
>
> Hi,
> the RIS format actually is a 'tagged text' file, with the tag being 2 characters, a space, a hyphen and a space, e.g.
> AU - Dostojevski
>
> So one way to deal with it would be to use the CISIS-utility 'ID2I' (also part of ABCD in the cgi-bin folder), which however expects the tag to be in the format of : !vXXX!
> So you would need to process the input RIS-file with a 'search and replace' action (available in most text-editors) to change AU- to v001! to put the authors in v1, and so on.
>
> This also requires all records to start with the same tag, so as to allow adding a 'record separator' with the same 'search and replace' tool, e.g.
> search : AU -
> replace with : !ID 000000
>                          AU -
>
> Well, I have never tried it but it should work in principle.
> In ABCD itself (utilities/import) there is a way of defining a table for conversion of text-input into ISIS-records, with the possibility to define tag-texts and the destination fields for each tag.
>
> Egbert de Smet
> Universiteit Antwerpen
> ________________________________________
> From: isis-users <isis-users-bounces+egbert.desmet=ua.ac.be at iccisis.org> on behalf of Adagilson Batista Bispo da Silva <adagilson at cpqam.fiocruz.br>
> Sent: Friday, March 9, 2018 9:15 PM
> To: 'isis-users'
> Subject: [Isis-users] Import RIS Files using MX
>
> Hello,
>
> I wonder if I can import RIS files using MX. Is it possible?
>
>
>
> Eu gostaria de saber se há como importar arquivos RIS para uma base CDS/ISIS usando MX. É possível?
>
>
>
> Adagilson Silva
>
> Instituto Aggeu Magalhães
>
> Pesquisa na Biblioteca
>
> http://bvsfiocruz.fiocruz.br/
> Repositório Institucional ARCA
> https://www.arca.fiocruz.br/
> Teses Fiocruz
> http://teses.icict.fiocruz.br/
> _______________________________________________
> isis-users mailing list
> isis-users at iccisis.org
> To manage your own subscription options go to: http://lists.iccisis.org/listinfo/isis-users
> Or contact Henk Rutten: hlrutten at xs4all.nl
> _______________________________________________
> isis-users mailing list
> isis-users at iccisis.org
> To manage your own subscription options go to: http://lists.iccisis.org/listinfo/isis-users
> Or contact Henk Rutten: hlrutten at xs4all.nl

-- 
   .^.                                .^.
   ( )                                ( )
   ===                                ===
  =[=]================================[=]=
   | |  Ernesto Spinak                | |
   | |  spinaker at adinet.com.uy        | |
   | |  Montevideo, Uruguay           | |
   | |  tel/fax  (598) 2622-3352      | |
   | |  celular  (598) 99612238      | |
  =[=]================================[=]=
   ===                                ===
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ER  -
TY  - JOUR
T1  - Carcinogenic liver fluke Opisthorchis viverrini oxysterols detected by LC-MS/MS survey of soluble fraction parasite extract
JF  - Parasitology International
VL  - 62
IS  - 6
SP  - 535
EP  - 542
PY  - 2013///
AU  - Vale, N.
AU  - Gouveia, M.J.
AU  - Botelho, M.
AU  - Sripa, B.
AU  - Suttiprapa, S.
AU  - Rinaldi, G.
AU  - Gomes, P.
AU  - Brindley, P.J.
AU  - Correia da Costa, J.M.
AD  - CIQUP, Chemistry and Biochemistry Department, Faculty of Sciences, University of Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal
AD  - Center for the Study of Animal Science, ICETA, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
AD  - INSA, Rua Alexandre Herculano. 321, 4000-055 Porto, Portugal
AD  - Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
AD  - Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
AD  - Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, Research Center for Neglected Tropical and Infectious Diseases, George Washington University, Washington, DC 20037, United States
AD  - Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo 11800, Uruguay
AB  - Liquid chromatography in tandem mass spectrometry (LC-MS/MS) has emerged as an informative tool to investigate oxysterols (oxidized derivatives of cholesterol) in helminth parasite associated cancers. Here, we used LC-MS/MS to investigate in soluble extracts of the adult developmental stage of Opisthorchis viverrini from experimentally infected hamsters. Using comparisons with known bile acids and the metabolites of estrogens, the LC-MS data indicated the existence of novel oxysterol derivatives in O. viverrini. Most of these derivatives were ramified at C-17, in similar fashion to bile acids and their conjugated salts. Several were compatible with the presence of an estrogen core, and/or hydroxylation of the steroid aromatic ring A, hydroxylation of both C-2 and C-3 of the steroid ring and further oxidation into an estradiol-2,3-quinone. © 2013 Published by Elsevier Ireland Ltd.
KW  - Bile acids
KW  - Flukes
KW  - Opisthorchis viverrini
KW  - Oxysterols
KW  - estrogen
KW  - oxysterol
KW  - article
KW  - controlled study
KW  - high performance liquid chromatography
KW  - nonhuman
KW  - Opisthorchis viverrini
KW  - priority journal
KW  - steroid hydroxylation
KW  - tandem mass spectrometry
KW  - Cricetinae
KW  - Fasciola hepatica
KW  - Opisthorchis viverrini
KW  - Vermes
N1  - Export Date: 22 November 2013
N1  - Source: Scopus
N1  - doi: 10.1016/j.parint.2013.08.001
N1  - Language of Original Document: English
N1  - Correspondence Address: Vale, N.; CIQUP, Chemistry and Biochemistry Department, Faculty of Sciences, University of Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal; email: nuno.vale at fc.up.pt
UR  - http://www.scopus.com/inward/record.url?eid=2-s2.0-84883274221&partnerID=40&md5=7548a71da16c50bac02b303b406c7396
ER  - 

TY  - JOUR
T1  - Activation of Toll-like receptor 2 increases macrophage resistance to HIV-1 infection
JF  - Immunobiology
VL  - 218
IS  - 12
SP  - 1529
EP  - 1536
PY  - 2013///
AU  - Victoria, S.
AU  - Temerozo, J.R.
AU  - Gobbo, L.
AU  - Pimenta-Inada, H.K.
AU  - Bou-Habib, D.C.
AD  - Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Av. Brasil 4365, Manguinhos - 21040-360, Rio de Janeiro, RJ, Brazil
AD  - Cell Biology Unit, Montevideo Pasteur Institute, Mataojo 2020, Montevideo, Uruguay
AD  - Laboratory of Translational Research, National Institute of Can-cer, R. André Cavalcanti 37, 20231-050 Rio de Janeiro, RJ, Brazil
AB  - Patients infected with HIV-1, the etiological agent of AIDS, have increased intestinal permeability, which allows for the passage of microbial products, including Toll-like receptor (TLR) ligands, into circulation. The exposure of HIV-1-infected cells to certain TLR agonists affects viral replication, but studies associating viral production with the activation of TLR2 in HIV-1-infected cells are rare and controversial. Here, we report that the TLR2 ligands Zymosan and Pam3CSK4 potently inhibit HIV-1 replication in acutely infected monocyte-derived macrophages and the exposure to TLR2 ligands prior to infection renders macrophages refractory to HIV-1 production. Macrophage treatment with Pam3CSK4 did not change the cellular expression of the HIV-1 entry receptors CD4 and CCR5. Both TLR2 ligands increased the macrophage production of β-chemokines and IL-10, and the blockage of these soluble factors prevented the inhibitory effect of TLR2 activation on HIV-1 replication. Our findings show that the direct engagement of TLR2 in HIV-1-infected macrophages increase cellular resistance to HIV-1 infection, and that controlling HIV-1 replication with agonists for TLR2 might have implications for the development of antiretroviral therapies. © 2013 Elsevier GmbH.
KW  - β-Chemokines
KW  - HIV
KW  - IL-10
KW  - Macrophages
KW  - Toll-like receptor
N1  - Export Date: 22 November 2013
N1  - Source: Scopus
N1  - doi: 10.1016/j.imbio.2013.06.006
N1  - Language of Original Document: English
N1  - Correspondence Address: Bou-Habib, D.C.; Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz/Fiocruz, Av. Brasil 4365, Manguinhos - Pav. Leonidas Deane/510, 21040-360 - Rio de Janeiro, RJ, Brazil; email: dumith at ioc.fiocruz.br
UR  - http://www.scopus.com/inward/record.url?eid=2-s2.0-84885927651&partnerID=40&md5=0170e318d5e8a67bedc11a6212001f52
ER  - 

TY  - JOUR
T1  - The suitability of three Galia melon cultivars and different types of cuts for the fresh-cut industry
JF  - Journal of the Science of Food and Agriculture
VL  - 93
IS  - 15
SP  - 3826
EP  - 3831
PY  - 2013///
AU  - Silveira, A.C.
AU  - Aguayo, E.
AU  - Artés, F.
AD  - Vegetable Production Department, Postharvest Division, Agronomy Faculty, Montevideo, Uruguay
AD  - Postharvest and Refrigeration Group, Department of Food Engineering, Technical University of Cartagena, Murcia, E-30203, Spain
AD  - Institute of Plant Biotechnology, Technical University of Cartagena, Murcia, E-30202, Spain
AB  - BACKGROUND: Melons (Cucumis melo L.) are widely cultivated in Mediterranean countries. For fresh-cut melon elaboration, factors such as type of cultivar and cut have a significant impact on final product quality. The quality parameters from long, medium and short shelf-life Galia melon cultivars, cut into different shapes such as slices, trapezoids and cylinders and stored up to 10 days at 5 °C, were evaluated in order to learn the suitability of these cultivars and type of cut for minimal processing. RESULTS: In general, long-life melon cultivar had a low respiration rate and ethylene emissions, and high tissue firmness, but low levels of glucose, fructose, vitamin C and flavor rating by consumers. However, despite having higher metabolic activity and susceptibility to microbial spoilage, the short shelf-life cultivar melon had higher firmness retention. This cultivar was characterized by its richness in glucose, fructose and vitamin C, and its sensory quality (flavor) was highly valued. In general, the medium cultivar had an intermediate behavior between long and short cultivars but without their positive attributes. As a consequence of the most intense damage, the cylindrical shape had higher metabolic activity, susceptibility to microbial spoilage and reduced appearance. CONCLUSIONS: In the long and medium-life cultivars studied, low flavor was the limiting factor to extend the shelf-life of fresh-cut melon while for the short-life cultivar the limiting factor was its susceptibility to bacterial growth. Cut types such as cylinders should be avoided. © 2013 Society of Chemical Industry.
KW  - Cucumis melo L. var. cantalupensis
KW  - Fresh-cut
KW  - Microbial quality
KW  - Sensory quality
KW  - Vitamin C content
N1  - Export Date: 22 November 2013
N1  - Source: Scopus
N1  - doi: 10.1002/jsfa.6306
N1  - Language of Original Document: English
N1  - Correspondence Address: Silveira, A.C.; Vegetable Production Department, Postharvest Division, Agronomy Faculty, Avenida Garzon 780, CP 12300, Montevideo, Uruguay; email: acsilver at fagro.edu.uy
UR  - http://www.scopus.com/inward/record.url?eid=2-s2.0-84886992270&partnerID=40&md5=38bc285e723db99256377ee22229e3d6
ER  - 

TY  - INPR
T1  - Prednisone in lupus nephritis: How much is enough?
JF  - Autoimmunity Reviews
PY  - 2013///
AU  - Ruiz-Irastorza, G.
AU  - Danza, A.
AU  - Perales, I.
AU  - Villar, I.
AU  - Garcia, M.
AU  - Delgado, S.
AU  - Khamashta, M.
AD  - Autoimmune Diseases Research Unit, Department of Internal Medicine, Biocruces Health Research Institute, Hospital Universitario Cruces, Spain
AD  - University of the Basque Country, Bizkaia, The Basque Country, Spain
AD  - Department of Internal Medicine, Hospital Pasteur, Montevideo, Uruguay
AD  - Facultad de Medicina, Universidad de la Republica, Uruguay
AD  - Service of Internal Medicine, Hospital Rey Juan Carlos, Madrid, Spain
AD  - Service of Nephrology, Hospital Universitario Cruces, Bizkaia, The Basque Country, Spain
AD  - Graham Hughes Lupus Research Laboratory, Division of Women's Health, The Rayne Institute, King's College, London, UK
AB  - Objective: To assess the effectiveness and safety of a protocol using medium doses of prednisone to treat lupus nephritis. Methods: Patients receiving the 'Cruces-protocol cohort' (CPC) were paired 1:2 with patients from the 'historic cohort' (HC). The CPC received medium doses of prednisone combined with methyl-prednisolone pulses, hydroxychloroquine and immunosuppressive drugs, usually cyclophosphamide. The HC received cyclophosphamide and high-dose prednisone. Partial and complete remission rates and glucocorticoid-related toxicity were assessed. Results: 15 CPC and 30 HC patients were analysed. The mean (SD) initial dose of prednisone was 22 (8) mg/d in the CPC vs. 49 (19) mg/d in the HC (p < 0.001). The 6-month mean (SD) cumulative dose of prednisone was 1.7 (0.5) g (average daily dose 9 mg) vs. 4.5 (2.1) g (average daily dose 25 mg), respectively (p < 0.001). The median cumulative dose of cyclophosphamide at six months was 3 (0-4.5) g in the CPC vs. 5 (0-16.8) in the HC (p < 0.001). 15/15 (100%) vs. 10/30 (33%) patients were treated with hydroxychloroquine (p < 0.001). At six months, 12/15 (80%) patients in the CPC achieved partial or complete remission vs. 14/30 (47%) in the HC (p = 0.015). At 12 months, 13/15 (87%) vs. 19/30 (63%) patients, respectively, were in complete or partial remission (p = 0.055). Toxicity attributable to glucocorticoids was observed in 1/15 (7%) vs. 20/30 (67%) patients, respectively (p < 0.0001). Conclusion: A combination of medium-dose prednisone, methylprednisolone pulses, cyclophosphamide and hydroxychloroquine is at least as effective in achieving remission of lupus nephritis as regimes containing high-dose prednisone and causes less toxicity. © 2013 Elsevier B.V. All rights reserved.
KW  - Adverse effects
KW  - Glucocorticoids
KW  - Hydroxychloroquine
KW  - Osteonecrosis
KW  - Osteoporosis
KW  - Systemic lupus erythematosus
N1  - Export Date: 22 November 2013
N1  - Source: Scopus
N1  - Article in Press
N1  - doi: 10.1016/j.autrev.2013.10.013
N1  - Language of Original Document: English
N1  - Correspondence Address: Ruiz-Irastorza, G.; Autoimmune Diseases Research Unit, Department of Internal Medicine, Biocruces Health Research Institemail: r.irastorza at euskaltel.net
UR  - http://www.scopus.com/inward/record.url?eid=2-s2.0-84887146221&partnerID=40&md5=2483363d57f4d28c3886f36d49add205

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ER  - |!ID000000
TY  - |!v005!
UR  - |!v008!
A2  - |!v010!
AU  - |!v010!
T1  - |!v012!
T2  - |!v013!
SP  - |!v014!
EP  - |!v015!
JF  - |!v030!
VL  - |!v031!
IS  - |!v032!
T3  - |!v053!
Y2  - |!v054!
CY  - |!v056!
N1  - |!v061!
PB  - |!v062!
PY  - |!v064!
AB  - |!v083!
KW  - |!v087!
AD  - |!v110!
JA  - |!v130!
SN  - |!v035!
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