[Isis-users] Jsonl files - import into ISIS
De Smet Egbert
egbert.desmet at uantwerpen.be
Sun Mar 17 16:58:11 CET 2019
Renate,
maybe an option is this :
- convert (with one of the several freely available converters) JSON to XML
- CISIS has a way to convert XML to ISIS based on a 'driver file' which does the mapping of tags to field-tags. E.g. mx has an input parameter 'XML=' :
xml[/1m]=<file>,<element>|
The problem is that there is no documentation whatsoever on this parameter... at least not as far as I can find in the CISIS manual.
Maybe Ernesto knows more about this or can find out...?
In fact there are more such hidden (unknown because undocumented) features of CISIS, which I think is really a pity, not to say a problem.
Egbert de Smet
Universiteit Antwerpen
________________________________
From: isis-users <isis-users-bounces+egbert.desmet=ua.ac.be at iccisis.org> on behalf of spinaker <spinaker at adinet.com.uy>
Sent: Sunday, March 17, 2019 3:18 PM
To: rmorgenstern at iway.na; isis-users at iccisis.org
Subject: Re: [Isis-users] Jsonl files - import into ISIS
Dear Renate
Concerning your 2nd question, how to clean fields with <> chars
a) prepare a text file, with this content
<|
>|
and save it with the name xxx.txt
b) now you create a gizmo file
mx seq=xxx.txt create=triang now
c) Then you apply this gizmo to your databse
mx your_base create=xxx1 now -all tell=1000 gizmo=triang,tag1,tag2 ... etc
where tag1,tag2 are the fileds concernet, ex: gizmo=triang,12,18,25
d) now you clean your database
mxcp xxx1 create=final clean tell=1000
ready !!! enjoy it
Now , let's see your first questions, about the conversion of a JSON text file into isis structure
You sent me a file with examples, I copied below the first record
Maybe there is some converter out there (I don't know) but we'd need at least the layout of the record, with definitions of the labels, then it would be possible to prepare a conversion procedure to substitute these labels with appropiate labels like examples below
!ID mmmmmm
!vXXX!...contents of tag XXX.............
!vYYY!...contents of tag YYY.............
...
Then you could use the CISIS program ID2I to convert the file , but first the first, do you have a definition of the layout?
Regards
Ernesto Spinak
________________________________
JSON RECORD
{"doi": "10.1080/21645515.2017.1330236",
"year": 2017,
"genre": "journal-article",
"is_oa": true,
"title": "Advancements in DNA vaccine vectors, non-mechanical delivery methods, and molecular adjuvants to increase immunogenicity",
"doi_url": "https://doi.org/10.1080/21645515.2017.1330236"<https://doi.org/10.1080/21645515.2017.1330236>,
"updated": "2018-06-19T00:17:12.337035",
"publisher": "Informa UK Limited", "z_authors":
[ {"given": "John J.",
"family": "Suschak",
"affiliation":
[ {"name": " U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA"} ]
},
{"given": "James A.",
"family": "Williams",
"affiliation":
[ {"name": " Nature Technology Corporation, Lincoln, NE, USA"}]},
{"given": "Connie S.", "family": "Schmaljohn", "affiliation": [{"name": " U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA"}]}],
"journal_name": "Human Vaccines & Immunotherapeutics",
"oa_locations":
[{"url": "http://europepmc.org/articles/pmc5718814?pdf=render"<http://europepmc.org/articles/pmc5718814?pdf=render>,
"pmh_id": "oai:pubmedcentral.nih.gov:5718814",
"is_best": true,
"license": "cc-by-nc-nd",
"updated": "2018-01-22T13:10:35.073612",
"version": "publishedVersion",
"evidence": "oa repository (via OAI-PMH title and first author match)",
"host_type":
"repository",
"url_for_pdf": "http://europepmc.org/articles/pmc5718814?pdf=render"<http://europepmc.org/articles/pmc5718814?pdf=render>,
"url_for_landing_page": "http://europepmc.org/articles/pmc5718814"<http://europepmc.org/articles/pmc5718814>}],
[https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/pmc-logo-share.png]<http://europepmc.org/articles/pmc5718814>
Advancements in DNA vaccine vectors, non-mechanical delivery methods, and molecular adjuvants... - Europe PMC Article - Europe PMC<http://europepmc.org/articles/pmc5718814>
europepmc.org
FULL TEXT Abstract: A major advantage of DNA vaccination is the ability to induce both humoral and cellular immune responses. DNA vaccines are currently used in...
"data_standard": 2,
"journal_is_oa": false,
"journal_issns": "2164-5515,2164-554X",
"published_date": "2017-06-12",
"best_oa_location": {"url": "http://europepmc.org/articles/pmc5718814?pdf=render"<http://europepmc.org/articles/pmc5718814?pdf=render>,
"pmh_id": "oai:pubmedcentral.nih.gov:5718814",
"is_best": true,
"license": "cc-by-nc-nd",
"updated": "2018-01-22T13:10:35.073612",
"version": "publishedVersion",
"evidence": "oa repository (via OAI-PMH title and first author match)", "host_type": "repository", "url_for_pdf": "http://europepmc.org/articles/pmc5718814? pdf=render"<http://europepmc.org/articles/pmc5718814? pdf=render>,
"url_for_landing_page": "http://europepmc.org/articles/pmc5718814"<http://europepmc.org/articles/pmc5718814>},
[https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/pmc-logo-share.png]<http://europepmc.org/articles/pmc5718814>
Advancements in DNA vaccine vectors, non-mechanical delivery methods, and molecular adjuvants... - Europe PMC Article - Europe PMC<http://europepmc.org/articles/pmc5718814>
europepmc.org
FULL TEXT Abstract: A major advantage of DNA vaccination is the ability to induce both humoral and cellular immune responses. DNA vaccines are currently used in...
"journal_is_in_doaj": false}
________________________________
El 14/03/2019 a las 3:46, Renate Morgenstern escribió:
Hi Ernesto,
Hope you are doing fine?
Is it possible to convert Jsonl files to ISIS? Please advise.
I am attaching one so that you can have a look at it.
It contains 2000 records. The whole file contains more than 100000 records.
Secondly, I am cleaning an ISIS database which comes from Winisis. I want to get rid of the <> around articles (the, an, an, der, die das, etc) from the title field.
Example: ^a<The> history of Africa
Is there an mx proc which I could use?
Thanks for your help in advance.
Renate
--
Renate Morgenstern
Tel.: +264 61 242124
Cell: +264 81 2910284
Fax: 088637518
Windhoek, Namibia
--
.^. .^.
( ) ( )
=== ===
=[=]================================[=]=
| | Ernesto Spinak | |
| | spinaker at adinet.com.uy<mailto:spinaker at adinet.com.uy> | |
| | Montevideo, Uruguay | |
| | tel/fax (598) 2622-3352 | |
| | celular (598) 99612238 | |
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