diff --git a/src/preprint-changes.xsl b/src/preprint-changes.xsl index 31a4e05778..8cf390def3 100644 --- a/src/preprint-changes.xsl +++ b/src/preprint-changes.xsl @@ -756,15 +756,22 @@ + + Competing interests: + + + No competing interests declared + + + + + + : - - Competing interests: - - @@ -1376,6 +1383,20 @@ + + + + + + ethics-statement + + + + + + + + sec element is not populated with any content. Either there's a mistake or the section should be removed. - sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? @@ -1230,6 +1230,10 @@ role="warning" id="sec-coi-2">sec has a title suggesting it's a competing interest statement. COI statements should be captured within author-notes, so this content should be moved into fn with the fn-type="coi-statement" within author-notes. + sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.) + sec element only contains a child def-list. This is therefore a glossary, not a sec. diff --git a/src/rp-schematron.sch b/src/rp-schematron.sch index bdc32431ab..f06ee164b3 100644 --- a/src/rp-schematron.sch +++ b/src/rp-schematron.sch @@ -675,12 +675,14 @@ [sec-empty] sec element is not populated with any content. Either there's a mistake or the section should be removed. - [sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? + [sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? [sec-coi] sec has a title suggesting it's a competing interest statement, but there is also a competing interest statement in author-notes. Are they duplicates? COI statements should be captured within author-notes, so this section should likely be deleted. [sec-coi-2] sec has a title suggesting it's a competing interest statement. COI statements should be captured within author-notes, so this content should be moved into fn with the fn-type="coi-statement" within author-notes. + [sec-ethics] sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.) + [sec-def-list] sec element only contains a child def-list. This is therefore a glossary, not a sec. [sec-glossary] sec element only contains a child glossary. Is it a redundant sec (which should be deleted)? Or perhaps it indicates the structure/hierarchy has been incorrectly captured. diff --git a/src/rp-schematron.xsl b/src/rp-schematron.xsl index 0f23a30784..1899c78930 100644 --- a/src/rp-schematron.xsl +++ b/src/rp-schematron.xsl @@ -5066,8 +5066,8 @@ - - + + sec-data-availability warning @@ -5099,6 +5099,17 @@ + + + sec-ethics + error + + + + [sec-ethics] sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.) + + + sec-def-list diff --git a/test/tests/preprint-changes/all/output.xml b/test/tests/preprint-changes/all/output.xml index 019b315a72..88e0fc7a91 100644 --- a/test/tests/preprint-changes/all/output.xml +++ b/test/tests/preprint-changes/all/output.xml @@ -68,7 +68,7 @@

Present address: Department of Biochemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland

Present address: Massachusetts Institute of Technology, Picower Institute for Learning and Memory, 43 Vassar St, Cambridge, MA 02139, United States

Present address: Vertex Pharmaceuticals, 50 Northern Avenue, Boston, Mass. 02210, United States

-

Competing Interest Statement: The authors have declared no competing interest.

+

Competing interests: No competing interests declared

diff --git a/test/tests/preprint-changes/article-meta-changes/output.xml b/test/tests/preprint-changes/article-meta-changes/output.xml index 9979404c6a..e286bfd0cf 100644 --- a/test/tests/preprint-changes/article-meta-changes/output.xml +++ b/test/tests/preprint-changes/article-meta-changes/output.xml @@ -50,7 +50,7 @@ -

Competing Interest Statement: The authors have declared no competing interest.

+

Competing interests: No competing interests declared

2024 13 diff --git a/test/tests/preprint-changes/author-notes-notes-handling/output.xml b/test/tests/preprint-changes/author-notes-notes-handling/output.xml index 3597675ed8..c9550305d1 100644 --- a/test/tests/preprint-changes/author-notes-notes-handling/output.xml +++ b/test/tests/preprint-changes/author-notes-notes-handling/output.xml @@ -3,7 +3,7 @@ -

Competing Interest Statement: The authors have declared no competing interest.

+

Competing interests: No competing interests declared

DRKS00021419 diff --git a/test/tests/preprint-changes/rearrange-back/output.xml b/test/tests/preprint-changes/rearrange-back/output.xml index af7dcefad1..55977a84e7 100644 --- a/test/tests/preprint-changes/rearrange-back/output.xml +++ b/test/tests/preprint-changes/rearrange-back/output.xml @@ -16,7 +16,7 @@ Something else

...

- + Additional information Funding @@ -41,9 +41,9 @@

All code and software needed to generate the results is available as part of public resources: LD score regression (https://github.com/bulik/ldsc), FUMA (https://fuma.ctglab.nl/), MiXeR (https://github.com/precimed/mixer), BM location (simulation, training, and model) [made public upon acceptance].

- + Additional files - + diff --git a/test/tests/preprint-changes/sec-ethics/input.xml b/test/tests/preprint-changes/sec-ethics/input.xml new file mode 100644 index 0000000000..37c920eaea --- /dev/null +++ b/test/tests/preprint-changes/sec-ethics/input.xml @@ -0,0 +1,13 @@ + + +ETHICS STATEMENT + +Human + + +Monkey + + +Machine + + \ No newline at end of file diff --git a/test/tests/preprint-changes/sec-ethics/output.xml b/test/tests/preprint-changes/sec-ethics/output.xml new file mode 100644 index 0000000000..52c6c20d0a --- /dev/null +++ b/test/tests/preprint-changes/sec-ethics/output.xml @@ -0,0 +1,13 @@ + + +ETHICS STATEMENT + +Human + + +Monkey + + +Machine + + \ No newline at end of file diff --git a/test/tests/rp/sec-checks/sec-data-availability/fail.xml b/test/tests/rp/sec-checks/sec-data-availability/fail.xml index 9df37441c9..11412a59d3 100644 --- a/test/tests/rp/sec-checks/sec-data-availability/fail.xml +++ b/test/tests/rp/sec-checks/sec-data-availability/fail.xml @@ -1,6 +1,6 @@
diff --git a/test/tests/rp/sec-checks/sec-data-availability/pass.xml b/test/tests/rp/sec-checks/sec-data-availability/pass.xml index 347fc88dd1..94aaa9f7c0 100644 --- a/test/tests/rp/sec-checks/sec-data-availability/pass.xml +++ b/test/tests/rp/sec-checks/sec-data-availability/pass.xml @@ -1,6 +1,6 @@
diff --git a/test/tests/rp/sec-checks/sec-data-availability/sec-data-availability.sch b/test/tests/rp/sec-checks/sec-data-availability/sec-data-availability.sch index 4264582c2f..94644eb645 100644 --- a/test/tests/rp/sec-checks/sec-data-availability/sec-data-availability.sch +++ b/test/tests/rp/sec-checks/sec-data-availability/sec-data-availability.sch @@ -146,7 +146,7 @@ - [sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? + [sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? diff --git a/test/tests/rp/sec-checks/sec-ethics/fail.xml b/test/tests/rp/sec-checks/sec-ethics/fail.xml new file mode 100644 index 0000000000..854f639dbf --- /dev/null +++ b/test/tests/rp/sec-checks/sec-ethics/fail.xml @@ -0,0 +1,17 @@ + + + +
+ + Ethics + +

Human subjects: Fresh tissue samples were obtained upon informed consent from patients undergoing surgery at the Gynecology Division of the European Institute of Oncology (Milan). Sample collection was performed under the protocol number R789-IEO approved by the Ethics Committee of the European Institute of Oncology.

+
+ +

Animal experimentation: All animal studies were performed following a protocol approved by the fully authorized animal facility of European Institute of Oncology and by the Italian Ministry of Health (as required by the Italian Law) (IACUCs number 1256/2015) and in accordance to EU directive 2010/63. Mouse tissues were obtained from Karolinska Institutet (Stockholm, Sweden) and IRCCS San Raffaele Scientific Institute (Milan, Italy), in accordance with Institutional Animal Care and Use Committees.

+
+
+
+
\ No newline at end of file diff --git a/test/tests/rp/sec-checks/sec-ethics/pass.xml b/test/tests/rp/sec-checks/sec-ethics/pass.xml new file mode 100644 index 0000000000..942b53e92b --- /dev/null +++ b/test/tests/rp/sec-checks/sec-ethics/pass.xml @@ -0,0 +1,17 @@ + + + +
+ + Ethics + +

Human subjects: Fresh tissue samples were obtained upon informed consent from patients undergoing surgery at the Gynecology Division of the European Institute of Oncology (Milan). Sample collection was performed under the protocol number R789-IEO approved by the Ethics Committee of the European Institute of Oncology.

+
+ +

Animal experimentation: All animal studies were performed following a protocol approved by the fully authorized animal facility of European Institute of Oncology and by the Italian Ministry of Health (as required by the Italian Law) (IACUCs number 1256/2015) and in accordance to EU directive 2010/63. Mouse tissues were obtained from Karolinska Institutet (Stockholm, Sweden) and IRCCS San Raffaele Scientific Institute (Milan, Italy), in accordance with Institutional Animal Care and Use Committees.

+
+
+
+
\ No newline at end of file diff --git a/test/tests/rp/sec-checks/sec-ethics/sec-ethics.sch b/test/tests/rp/sec-checks/sec-ethics/sec-ethics.sch new file mode 100644 index 0000000000..e5499ea73d --- /dev/null +++ b/test/tests/rp/sec-checks/sec-ethics/sec-ethics.sch @@ -0,0 +1,157 @@ + + eLife reviewed preprint schematron + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + [sec-ethics] sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.) + + + + + sec must be present. + + + \ No newline at end of file diff --git a/test/xspec/preprint-changes.xspec b/test/xspec/preprint-changes.xspec index 55e202a35d..adc001a046 100644 --- a/test/xspec/preprint-changes.xspec +++ b/test/xspec/preprint-changes.xspec @@ -128,6 +128,10 @@ + + + + diff --git a/test/xspec/rp-schematron.sch b/test/xspec/rp-schematron.sch index b8f1a6dbfc..d2c8b7cba2 100644 --- a/test/xspec/rp-schematron.sch +++ b/test/xspec/rp-schematron.sch @@ -904,12 +904,14 @@ sec element is not populated with any content. Either there's a mistake or the section should be removed. - sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? + sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? sec has a title suggesting it's a competing interest statement, but there is also a competing interest statement in author-notes. Are they duplicates? COI statements should be captured within author-notes, so this section should likely be deleted. sec has a title suggesting it's a competing interest statement. COI statements should be captured within author-notes, so this content should be moved into fn with the fn-type="coi-statement" within author-notes. + sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.) + sec element only contains a child def-list. This is therefore a glossary, not a sec. sec element only contains a child glossary. Is it a redundant sec (which should be deleted)? Or perhaps it indicates the structure/hierarchy has been incorrectly captured. diff --git a/test/xspec/rp-schematron.xspec b/test/xspec/rp-schematron.xspec index e8a69d31b2..694fbcfc9d 100644 --- a/test/xspec/rp-schematron.xspec +++ b/test/xspec/rp-schematron.xspec @@ -2103,6 +2103,16 @@ + + + + + + + + + +