jdone
commented
11 years ago Hi Kimberly,
I have updated the format script for the XML uploads; you may want to try today's version. The new uploads are treated as UTF-8 not as text so there may be differences.
James
On Tue, Aug 6, 2013 at 7:28 AM, vanaukenk notifications@github.com wrote:
Hi James,
Thanks for allowing curators to upload papers to GOAT again.
I just wanted to check with you about something that seems different between PLoS XMLs that you uploaded for me last month vs what I uploaded since late last week.
In the two XMLs that I uploaded, there is a space after mentions of a Figure. For example, in the newly uploaded paper journal.pgen.1003315, the statement below refers to Figure 4 and there is a space between 4 and the closed parenthesis:
Treatment with fos-1 RNAi markedly increased intestinal Pkreg-1::venus expression even in the absence of Cu2+ (Figure 4 ).
If I annotate this sentence, no visible hyperlink is created. Here is the annotation:
Date: 2013-08-06T14:15:25.805Z DocID: journal.pgen.1003315 Curator: vanauken Sentence: Treatment with fos-1 RNAi markedly increased intestinal Pkreg-1::venus expression even in the absence of Cu2+ (Figure 4 ). GO Term(s): negative regulation of transcription from RNA polymerase II promoter (GO:0000122), GO Evidence Code(s):IMP :Inferred from Mutant Phenotype, with Gene(s): fos-1|WBGene00001345 Comment(s):
In a previous PLoS XML that you uploaded for me last month, journal.pbio.0020257, there is no space after the Figure numbers:
The RNAi of elo-6 significantly reduced the amount of only C17ISO, while the RNAi of elo-5 dramatically reduced quantities of both C15ISO and C17ISO (Figure 3).
And a visible hyperlink is created up until the word Figure. Here's this annotation:
Date: 2013-07-26T14:52:30.660Z DocID: journal.pbio.0020257 Curator: vanauken Sentence: The RNAi of elo-6 significantly reduced the amount of only C17ISO, while the RNAi of elo-5 dramatically reduced quantities of both C15ISO and C17ISO (Figure 3). GO Term(s): methyl-branched fatty acid biosynthetic process (GO:1902321), GO Evidence Code(s):IMP :Inferred from Mutant Phenotype, with Gene(s): elo-5|WBGene00001243;elo-6|WBGene00001244 Comment(s):
I was wondering if you had any thoughts about why this is different. It does really help to have the hyperlinks visible in the document, even if they don't include the full Figure mention.
Thanks, --Kimberly
— Reply to this email directly or view it on GitHubhttps://github.com/WormBase/Literature-Annotation-Tool/issues/20 .
vanaukenk
Hi James,
Thanks for allowing curators to upload papers to GOAT again.
I just wanted to check with you about something that seems different between PLoS XMLs that you uploaded for me last month vs what I uploaded since late last week.
In the two XMLs that I uploaded, there is a space after mentions of a Figure. For example, in the newly uploaded paper journal.pgen.1003315, the statement below refers to Figure 4 and there is a space between 4 and the closed parenthesis:
Treatment with fos-1 RNAi markedly increased intestinal Pkreg-1::venus expression even in the absence of Cu2+ (Figure 4 ).
If I annotate this sentence, no visible hyperlink is created. Here is the annotation:
Date: 2013-08-06T14:15:25.805Z DocID: journal.pgen.1003315 Curator: vanauken Sentence: Treatment with fos-1 RNAi markedly increased intestinal Pkreg-1::venus expression even in the absence of Cu2+ (Figure 4 ). GO Term(s): negative regulation of transcription from RNA polymerase II promoter (GO:0000122), GO Evidence Code(s):IMP :Inferred from Mutant Phenotype, with Gene(s): fos-1|WBGene00001345 Comment(s):
In a previous PLoS XML that you uploaded for me last month, journal.pbio.0020257, there is no space after the Figure numbers:
The RNAi of elo-6 significantly reduced the amount of only C17ISO, while the RNAi of elo-5 dramatically reduced quantities of both C15ISO and C17ISO (Figure 3).
And a visible hyperlink is created up until the word Figure. Here's this annotation:
Date: 2013-07-26T14:52:30.660Z DocID: journal.pbio.0020257 Curator: vanauken Sentence: The RNAi of elo-6 significantly reduced the amount of only C17ISO, while the RNAi of elo-5 dramatically reduced quantities of both C15ISO and C17ISO (Figure 3). GO Term(s): methyl-branched fatty acid biosynthetic process (GO:1902321), GO Evidence Code(s):IMP :Inferred from Mutant Phenotype, with Gene(s): elo-5|WBGene00001243;elo-6|WBGene00001244 Comment(s):
I was wondering if you had any thoughts about why this is different. It does really help to have the hyperlinks visible in the document, even if they don't include the full Figure mention.
Thanks, --Kimberly