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<p>Renate,</p>
<p><br>
</p>
<p>maybe an option is this : <br>
</p>
<p>- convert (with one of the several freely available converters) JSON to XML</p>
<p>- 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=' :
<br>
</p>
<p><span>xml[/1m]=<file>,<element>|</span><br>
</p>
<p><br>
</p>
<p>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.</p>
<p>Maybe Ernesto knows more about this or can find out...?</p>
<p>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.</p>
<p><br>
</p>
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<div class="BodyFragment"><font size="2"><span style="font-size:10pt;">
<div class="PlainText">Egbert de Smet<br>
Universiteit Antwerpen</div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> isis-users <isis-users-bounces+egbert.desmet=ua.ac.be@iccisis.org> on behalf of spinaker <spinaker@adinet.com.uy><br>
<b>Sent:</b> Sunday, March 17, 2019 3:18 PM<br>
<b>To:</b> rmorgenstern@iway.na; isis-users@iccisis.org<br>
<b>Subject:</b> Re: [Isis-users] Jsonl files - import into ISIS</font>
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<div class="moz-cite-prefix">Dear Renate</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix"><u>Concerning your 2nd question, how to clean fields with <> chars</u></div>
<div class="moz-cite-prefix">a) prepare a text file, with this content</div>
<div class="moz-cite-prefix"> <|<br>
>|<br>
and save it with the name xxx.txt</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">b) now you create a gizmo file</div>
<div class="moz-cite-prefix"> mx seq=xxx.txt create=triang now</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">c) Then you apply this gizmo to your databse</div>
<div class="moz-cite-prefix"> mx your_base create=xxx1 now -all tell=1000 gizmo=triang,tag1,tag2 ... etc
<br>
</div>
<div class="moz-cite-prefix"> where tag1,tag2 are the fileds concernet, ex: gizmo=triang,12,18,25<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">d) now you clean your database</div>
<div class="moz-cite-prefix"> mxcp xxx1 create=final clean tell=1000</div>
<div class="moz-cite-prefix"> ready !!! enjoy it<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix"><u>Now , let's see your first questions, about the conversion of a JSON text file into isis structure</u></div>
<div class="moz-cite-prefix">You sent me a file with examples, I copied below the first record</div>
<div class="moz-cite-prefix">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<br>
</div>
<div class="moz-cite-prefix"><font size="+1" face="Courier New,
Courier, monospace">!ID mmmmmm<br>
!vXXX!...contents of tag XXX.............<br>
!vYYY!...contents of tag YYY.............</font><br>
...</div>
<div class="moz-cite-prefix">Then you could use the CISIS program ID2I to convert the file , but first the first, do you have a definition of the layout?</div>
<div class="moz-cite-prefix">Regards</div>
<div class="moz-cite-prefix">Ernesto Spinak</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">
<hr width="100%" size="2">
<font face="Courier New, Courier,
monospace"><b>JSON RECORD</b><br>
</font></div>
<div class="moz-cite-prefix"><font face="Courier New, Courier,
monospace">{"doi": "10.1080/21645515.2017.1330236",
<br>
"year": 2017, <br>
"genre": "journal-article", <br>
"is_oa": true, <br>
"title": "Advancements in DNA vaccine vectors, non-mechanical delivery methods, and molecular adjuvants to increase immunogenicity",
<br>
"doi_url": <a class="moz-txt-link-rfc2396E" href="https://doi.org/10.1080/21645515.2017.1330236" id="LPlnk915898" previewremoved="true">
"https://doi.org/10.1080/21645515.2017.1330236"</a>, <br>
"updated": "2018-06-19T00:17:12.337035", <br>
"publisher": "Informa UK Limited", "z_authors": <br>
[ {"given": "John J.", <br>
"family": "Suschak", <br>
"affiliation": <br>
[ {"name": " U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA"} ]<br>
}, <br>
{"given": "James A.", <br>
"family": "Williams", <br>
"affiliation": <br>
[ {"name": " Nature Technology Corporation, Lincoln, NE, USA"}]}, <br>
{"given": "Connie S.", "family": "Schmaljohn", "affiliation": [{"name": " U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA"}]}],
<br>
"journal_name": "Human Vaccines & Immunotherapeutics", <br>
"oa_locations": <br>
[{"url": <a class="moz-txt-link-rfc2396E" href="http://europepmc.org/articles/pmc5718814?pdf=render" id="LPlnk733803" previewremoved="true">
"http://europepmc.org/articles/pmc5718814?pdf=render"</a>, <br>
"pmh_id": "oai:pubmedcentral.nih.gov:5718814", <br>
"is_best": true, <br>
"license": "cc-by-nc-nd", <br>
"updated": "2018-01-22T13:10:35.073612", <br>
"version": "publishedVersion", <br>
"evidence": "oa repository (via OAI-PMH title and first author match)", <br>
"host_type": <br>
"repository", <br>
"url_for_pdf": <a class="moz-txt-link-rfc2396E" href="http://europepmc.org/articles/pmc5718814?pdf=render" id="LPlnk894348" previewremoved="true">
"http://europepmc.org/articles/pmc5718814?pdf=render"</a>,<br>
"url_for_landing_page": <a class="moz-txt-link-rfc2396E" href="http://europepmc.org/articles/pmc5718814" id="LPlnk515371" previewremoved="true">
"http://europepmc.org/articles/pmc5718814"</a>}],
<div id="LPBorder_GT_15528380078140.23248962666493167" style="margin-bottom: 20px; overflow: auto; width: 100%; text-indent: 0px;">
<table id="LPContainer_15528380078070.709647044369592" style="width: 90%; background-color: rgb(255, 255, 255); position: relative; overflow: auto; padding-top: 20px; padding-bottom: 20px; margin-top: 20px; border-top: 1px dotted rgb(200, 200, 200); border-bottom: 1px dotted rgb(200, 200, 200);" role="presentation" cellspacing="0">
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<div id="LPImageContainer_15528380078090.32887211057262056" style="background-color: rgb(255, 255, 255); height: 131px; position: relative; margin: auto; display: table; width: 250px;">
<a id="LPImageAnchor_15528380078100.4201015665979263" style="display: table-cell; text-align: center;" href="http://europepmc.org/articles/pmc5718814" target="_blank"><img style="display: inline-block; max-width: 250px; max-height: 250px; height: 131px; width: 250px; border-width: 0px; vertical-align: bottom;" aria-label="Preview image with link selected. Double-tap to open the link." id="LPThumbnailImageID_15528380078100.25815706147076634" width="250" height="131" src="https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/pmc-logo-share.png"></a></div>
</td>
<td id="TextCell_15528380078110.46827222098584265" style="vertical-align: top; position: relative; padding: 0px; display: table-cell;" colspan="2">
<div id="LPRemovePreviewContainer_15528380078110.8179264990965549"></div>
<div id="LPTitle_15528380078110.4685060281916138" style="top: 0px; color: rgb(0, 120, 215); font-weight: 400; font-size: 21px; font-family: "wf_segoe-ui_light", "Segoe UI Light", "Segoe WP Light", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; line-height: 21px;">
<a id="LPUrlAnchor_15528380078120.7962610326675116" style="text-decoration: none;" href="http://europepmc.org/articles/pmc5718814" target="_blank">Advancements in DNA vaccine vectors, non-mechanical delivery methods, and molecular adjuvants... - Europe PMC
Article - Europe PMC</a></div>
<div id="LPMetadata_15528380078120.7450338384092042" style="margin: 10px 0px 16px; color: rgb(102, 102, 102); font-weight: 400; font-family: "wf_segoe-ui_normal", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; line-height: 14px;">
europepmc.org</div>
<div id="LPDescription_15528380078130.7868320962106601" style="display: block; color: rgb(102, 102, 102); font-weight: 400; font-family: "wf_segoe-ui_normal", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; line-height: 20px; max-height: 100px; overflow: hidden;">
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...</div>
</td>
</tr>
</tbody>
</table>
</div>
<br>
"data_standard": 2, <br>
"journal_is_oa": false, <br>
"journal_issns": "2164-5515,2164-554X", <br>
"published_date": "2017-06-12", <br>
"best_oa_location": {"url": <a class="moz-txt-link-rfc2396E" href="http://europepmc.org/articles/pmc5718814?pdf=render" id="LPlnk193718" previewremoved="true">
"http://europepmc.org/articles/pmc5718814?pdf=render"</a>, <br>
"pmh_id": "oai:pubmedcentral.nih.gov:5718814", <br>
"is_best": true, <br>
"license": "cc-by-nc-nd", <br>
"updated": "2018-01-22T13:10:35.073612", <br>
"version": "publishedVersion", <br>
"evidence": "oa repository (via OAI-PMH title and first author match)", "host_type": "repository", "url_for_pdf":
<a class="moz-txt-link-rfc2396E" href="http://europepmc.org/articles/pmc5718814? pdf=render" id="LPlnk430578" previewremoved="true">
"http://europepmc.org/articles/pmc5718814? pdf=render"</a>,<br>
"url_for_landing_page": <a class="moz-txt-link-rfc2396E" href="http://europepmc.org/articles/pmc5718814" id="LPlnk607843" previewremoved="true">
"http://europepmc.org/articles/pmc5718814"</a>},
<div id="LPBorder_GT_15528380379280.6954339585349754" style="margin-bottom: 20px; overflow: auto; width: 100%; text-indent: 0px;">
<table id="LPContainer_15528380379250.8511200072174321" style="width: 90%; background-color: rgb(255, 255, 255); position: relative; overflow: auto; padding-top: 20px; padding-bottom: 20px; margin-top: 20px; border-top: 1px dotted rgb(200, 200, 200); border-bottom: 1px dotted rgb(200, 200, 200);" role="presentation" cellspacing="0">
<tbody>
<tr style="border-spacing: 0px;" valign="top">
<td id="ImageCell_15528380379250.5039266023842951" style="width: 250px; position: relative; display: table-cell; padding-right: 20px;" colspan="1">
<div id="LPImageContainer_15528380379250.4995651720675267" style="background-color: rgb(255, 255, 255); height: 131px; position: relative; margin: auto; display: table; width: 250px;">
<a id="LPImageAnchor_15528380379250.26645472551331195" style="display: table-cell; text-align: center;" href="http://europepmc.org/articles/pmc5718814" target="_blank"><img style="display: inline-block; max-width: 250px; max-height: 250px; height: 131px; width: 250px; border-width: 0px; vertical-align: bottom;" aria-label="Preview image with link selected. Double-tap to open the link." id="LPThumbnailImageID_15528380379260.8398968953175004" width="250" height="131" src="https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/pmc-logo-share.png"></a></div>
</td>
<td id="TextCell_15528380379270.3407855361770262" style="vertical-align: top; position: relative; padding: 0px; display: table-cell;" colspan="2">
<div id="LPRemovePreviewContainer_15528380379270.43569128835101556"></div>
<div id="LPTitle_15528380379270.8137329409143453" style="top: 0px; color: rgb(0, 120, 215); font-weight: 400; font-size: 21px; font-family: "wf_segoe-ui_light", "Segoe UI Light", "Segoe WP Light", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; line-height: 21px;">
<a id="LPUrlAnchor_15528380379270.5603033634103929" style="text-decoration: none;" href="http://europepmc.org/articles/pmc5718814" target="_blank">Advancements in DNA vaccine vectors, non-mechanical delivery methods, and molecular adjuvants... - Europe PMC
Article - Europe PMC</a></div>
<div id="LPMetadata_15528380379270.20739125147432458" style="margin: 10px 0px 16px; color: rgb(102, 102, 102); font-weight: 400; font-family: "wf_segoe-ui_normal", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; line-height: 14px;">
europepmc.org</div>
<div id="LPDescription_15528380379280.9265939486350954" style="display: block; color: rgb(102, 102, 102); font-weight: 400; font-family: "wf_segoe-ui_normal", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; line-height: 20px; max-height: 100px; overflow: hidden;">
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...</div>
</td>
</tr>
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</table>
</div>
<br>
"journal_is_in_doaj": false}</font><br>
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<div class="moz-cite-prefix">El 14/03/2019 a las 3:46, Renate Morgenstern escribió:<br>
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<blockquote type="cite">
<div><span>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
Hi Ernesto,</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
<br>
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<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
Hope you are doing fine?</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
Is it possible to convert Jsonl files to ISIS? Please advise.</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
I am attaching one so that you can have a look at it.</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
It contains 2000 records. The whole file contains more than 100000 records.</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
<br>
</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
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.</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
Example: ^a<The> history of Africa</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
Is there an mx proc which I could use?</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
<br>
</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
Thanks for your help in advance.</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">
<br>
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<pre><span style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:16px">Renate</span></pre>
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<td>Renate Morgenstern<br>
Tel.: +264 61 242124<br>
Cell: +264 81 2910284<br>
Fax: 088637518<br>
Windhoek, Namibia </td>
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<pre class="moz-signature" cols="72">--
.^. .^.
( ) ( )
=== ===
=[=]================================[=]=
| | Ernesto Spinak | |
| | <a class="moz-txt-link-abbreviated" href="mailto:spinaker@adinet.com.uy">spinaker@adinet.com.uy</a> | |
| | Montevideo, Uruguay | |
| | tel/fax (598) 2622-3352 | |
| | celular (598) 99612238 | |
=[=]================================[=]=
=== ===
( ) ( )
V V </pre>
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