Doc update

README.md

@@ -77,7 +77,7 @@ The PMC Open Access Subset is one part of the PMC Article Datasets
 
 This version takes XML version as source, benefiting from the structured text
 to split the articles in parts, naming the introduction, methods, results,
-discussion and conclusion, and refers with keywords in the text to external or internal
+discussion and conclusion, and reference with keywords in the text to external or internal
 resources (articles, figures, tables, formulas, boxed-text, quotes, code, footnotes, chemicals, graphics, medias).
 
 The dataset was initially created with relation-extraction tasks in mind, between the references in text and the content of the
@@ -112,27 +112,11 @@ a corpus of pre-annotated text for other tasks (e.g. figure caption to graphic,
 - "box":          List of \<boxed-text\> elements of the article.
 - "code":         List of \<code\> elements of the article.
 - "quote":        List of \<disp-quote\> and \<speech\> elements of the article.
-- "chem":         List of \<chem-struct-wrap\> elements of the article.
+- "chemical":     List of \<chem-struct-wrap\> elements of the article.
 - "supplementary": List of \<supplementary-material\> and \<inline-supplementary-material\> elements of the article.
 - "footnote":      List of \<fn-group\> and \<table-wrap-foot\> elements of the article.
 - "graphic":       List of \<graphic\> and \<inline-graphic\> elements of the article.
 - "media":         List of \<media\> and \<inline-media\> elements of the article.
-
-- "references": Lists of references in the order found in the corresponding categories
-	- "pmid_ref":  PMIDs of other articles.                                In text, replaced by " ##REF## "
-	- "unknown_pub_ref":  0-indexed idx of the article in "unknown_pub".   In text, replaced by " ##UREF## "
-	- "figure_ref":  0-indexed idx of the figures in "figure"              In text, replaced by " ##FIG## "
-	- "table_ref":   0-indexed idx of the tables in "table"                In text, replaced by " ##TAB## "
-	- "formula_ref": 0-indexed idx of the formulas in "formula"            In text, replaced by " ##FORMU## "
-	- "box_ref":     0-indexed idx of the box in "box"                     In text, replaced by " ##BOX## "
-	- "code_ref":    0-indexed idx of the code in "code"                   In text, replaced by " ##CODE## "
-	- "quote_ref":   0-indexed idx of the quote in "quote"                 In text, replaced by " ##QUOTE## "
-	- "chem_ref":    0-indexed idx of the chemical in "chem"               In text, replaced by " ##CHEM## "
-	- "supplementary_ref": 0-indexed idx of the figure in "supplementary"  In text, replaced by " ##SUPPL## "
-	- "footnote_ref": 0-indexed idx of the footnote in "footnote"          In text, replaced by " ##FOOTN## "
-	- "graphic_ref":  0-indexed idx of the graphics in "graphics"          In text, replaced by " ##GRAPH## "
-	- "media_ref":    0-indexed idx of the medias in "medias"              In text, replaced by " ##MEDIA## "
-- "references_text": For each reference in "references", the corresponding text that the reference keywords replaced.
 - "glossary": Glossary if found in the XML
 - "unknown_references": JSON of a dictionnary of each "tag":"text" for the reference that did not indicate a PMID
 - "n_references": Total number of references and unknown references
@@ -142,6 +126,7 @@ a corpus of pre-annotated text for other tasks (e.g. figure caption to graphic,
 - "citation": Citation of the article
 - "package_file": path to the folder containing the graphics and media files of the article (to append to the base URL: ftp.ncbi.nlm.nih.gov/pub/pmc/)
 
+In text, the references are in the form ##KEYWORD##IDX_REF##OLD_TEXT##, with keywords (REF, UREF, FIG, TAB, FORMU, BOX, CODE, QUOTE, CHEM, SUPPL, FOOTN, GRAPH, MEDIA) referencing respectively to "pubmed articles" (external), "unknown_references", "figure", "table", "formula", "box", "code", "quote", "chem", "supplementary", "footnote", "graphic" and "media".
 ### Data Splits
 
 [Needs More Information]
@@ -204,13 +189,13 @@ future version.
 
 [Needs More Information]
 
-### Preprocessing advices
+### Preprocessing recommendations
 
 - Filter out empty contents.
 - Remove unwanted references from the text, and replace either by the "references_text" or by the reference content itself.
 - Unescape HTML special characters: `import html; html.unescape(my_text)`
 - Remove superfluous line break in text.
-- Remove XML tags / replace by special tokens (\<italic\>, \<sup\>, \<sub\>, ...).
+- Remove XML tags (\<italic\>, \<sup\>, \<sub\>, ...), replace by special tokens? 
 - Join the items of the contents' lists.
 
 ## Additional Information

pmc_open_access_xml.py

@@ -75,7 +75,7 @@ REFS_KEYS     = ["pmid_ref", "unknown_pub_ref", "figure_ref", "table_ref", "form
                  "quote_ref", "chem_ref", "supplementary_ref", "footnote_ref", "graphic_ref", "media_ref"]
 CONTENT_KEYS  = ["introduction", "methods", "results", "discussion", "conclusion",
                  "front", "body", "back", "figure", "table", "formula", "box",
-                 "code", "quote", "chem", "supplementary", "footnote"]
+                 "code", "quote", "chemical", "supplementary", "footnote"]
 begin_doc_rgx = re.compile("""<!DOCTYPE.*""")
 def clean_raw(xml_text):
     """
@@ -434,7 +434,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                     "box":           datasets.features.Sequence(datasets.Value("string")),
                     "code":          datasets.features.Sequence(datasets.Value("string")),
                     "quote":         datasets.features.Sequence(datasets.Value("string")),
-                    "chem":          datasets.features.Sequence(datasets.Value("string")),
+                    "chemical":      datasets.features.Sequence(datasets.Value("string")),
                     "supplementary": datasets.features.Sequence(datasets.Value("string")),
                     "footnote":      datasets.features.Sequence(datasets.Value("string")),
                     "graphic":       datasets.features.Sequence(datasets.Value("string")),
@@ -571,7 +571,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                         "box":           content_d["box"],
                         "code":          content_d["code"],
                         "quote":         content_d["quote"],
-                        "chem":          content_d["chem"],
+                        "chemical":      content_d["chemical"],
                         "supplementary": content_d["supplementary"],
                         "footnote":      content_d["footnote"],
                         "graphic":       content_d["graphic"],
@@ -633,7 +633,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                     "box":           content_d["box"],
                     "code":          content_d["code"],
                     "quote":         content_d["quote"],
-                    "chem":          content_d["chem"],
+                    "chemical":      content_d["chemical"],
                     "supplementary": content_d["supplementary"],
                     "footnote":      content_d["footnote"],
                     "graphic":       content_d["graphic"],