Merge pull request #562 from hed-standard/develop

Fixed links and other typos

docs/source/01_Introduction.md

@@ -50,7 +50,7 @@ As the name HED implies, much of the HED framework focuses on
 associating metadata with the experimental timeline to make datasets analysis-ready and
 machine-actionable. However, HED annotations and framework can be used to incorporate 
 other types of metadata into analysis by providing a common API (Application Programming 
-Interface) for building inter-operable tools. 
+Interface) for building interoperable tools. 
 
 This specification describes the official release of third 
 generation of HED or HED-3G, which is HED version 8.0.0. 

docs/source/03_HED_formats.md

@@ -114,8 +114,8 @@ Together with [**the epilogue**](./03_HED_formats.md#3129-the-epilogue) section,
 the contents are used by tools to provide information about the schema to the users.
 
 The prologue may only contain the following: letters, digits, blank, comma, newline,
-+, -, :, ;, ., /, (, ), ?, *, %, $, @ or
-a [**SCHEMA_CHARACTER_INVALID**](./Appendix_B.md#schema_character_invalid) error occurs.
++, -, :, ;, ., /, (, ), ?, *, %, $, @. 
+If other characters appear, a [**SCHEMA_CHARACTER_INVALID**](./Appendix_B.md#schema_character_invalid) error occurs.
 
 
 #### 3.1.2.3. The schema section
@@ -237,7 +237,8 @@ for information and a listing of schema attributes and their respective properti
 The epilogue should give license information, acknowledgments, and references.
 
 The epilogue may only contain the following: letters, digits, blank, comma, newline,
-+, -, :, ;, ., /, (, ), ?, *, %, $, @ or
++, -, :, ;, ., /, (, ), ?, *, %, $, @,
+If other characters appear, 
 a [**SCHEMA_CHARACTER_INVALID**](./Appendix_B.md#schema_character_invalid) error occurs.
 
 
@@ -685,7 +686,7 @@ It is needed so that term search works correctly.
 Tag extensions should follow the same naming conventions as
 those for schema nodes. 
 See [**3.1.3. Naming conventions**](#313-naming-conventions) for more information about HED naming conventions.
-A [**STYLE_WARNING**](Appendix_B.md#style_warning) warning is
+A [**STYLE_WARNING**](Appendix_B.md#style_warning) is
 issued for extension tags that do not follow the HED naming convention.
 
 Users should not use tag extension unless necessary for their application,
@@ -1145,22 +1146,24 @@ This description of tabular files conforms to that used by [**BIDS**](https://bi
 
 Generally each row in a tabular file represents an item and the columns values provide properties of that item.
 The most common HED-annotated tabular files represent event markers in an experiment (e.g., BIDS `events.tsv` files).
-In this case each row in represents a time at which something happened.
+In this case each row represents a time at which something happened.
 
 Another common HED-annotated tabular file represents experiment participants
 (e.g., BIDS `participants.tsv`).
 Each row in the file represents a participant, and the columns provide
 characteristics or other information about the participant identified in that row.
 
-The `events.tsv` and the `participants.tsv` are representative of two distinct types
-of tabular files: ones representing time markers and those representing other types of information.
-To be recognized as having time-markers, the first column of the file must be `onset`.
-Non-time marker files cannot use the `Onset`, `Offset`, or `Inset` tags as these
-tags are reserved for annotations of time processes.
+The `events.tsv` files are tabular files representing markers on a timeline.
+This type of tabular file must have `onset` as the first column,
+and HED tools use the time values in this column to resolve `Onset`, `Offset` and `Inset`.
+In contrast, the `participants.tsv` file, which contains information about the
+experimental participants, is representative of a non time-marker file.
+Non time-marker files cannot use the `Onset`, `Offset`, or `Inset` tags as these
+tags are reserved for annotations of time processes and cannot be resolved if there is no time.
 
 In any case, the general strategy for validation or other processing is:
-1. Process the individual components of the HED annotation (tag and string level processing).
-2. Assemble the component annotations for a row (event or row level processing).
+1. Process the individual components of the HED annotation (tag-level and string-level processing).
+2. Assemble the component annotations for a row (event-level or row-level processing).
 3. Check consistency and relationships among the row annotations (file-level processing).
 
 See [**BIDS tabular files**](06_Infrastructure_and_tools.md#631-bids-tabular-files) for
@@ -1176,7 +1179,7 @@ If the first column is not called `onset`, the assembled annotation for
 the tabular file cannot contain any of the tags `Onset`, `Offset`, or `Inset`.
 
 Definitions many not appear in the `HED` column of a tabular file or
-in any entry of a JSON sidecar corresponding that contains items other than definitions.
+in any entry of a JSON sidecar that contains items other than definitions.
 
 See [**DEFINITION_INVALID**](./Appendix_B.md#definition_invalid)
 and [**ONSET_OFFSET_INSET_ERROR**](./Appendix_B.md#onset_offset_inset_error) for information.

docs/source/04_Basic_annotation.md

@@ -15,7 +15,7 @@ following (or preceding) event markers. The addition of HED context, allows info
 about events that occur over extended periods of time to propagate to intermediate time points. 
 [**Chapter 5: Advanced annotation**](05_Advanced_annotation.md#5-advanced-annotation) 
 develops the HED concepts needed to capture these advanced models of events as well as event
-and task inter-relationships. 
+and task interrelationships. 
 
 
 ## 4.1. Instantaneous events

docs/source/06_Infrastructure_and_tools.md

@@ -7,7 +7,7 @@ its integration into other systems such as [**BIDS**](https://bids.neuroimaging.
 
 In general, tools should either explicitly call HED validation to assure that the input
 tag strings are valid or should make explicit that they assume the HED has already been validated.
-Most tools will use the later approach. 
+Most tools will use the latter approach. 
 
 See [**3.2. Annotation formats**](./03_HED_formats.md#32-annotation-formats)
 for more detailed specifications of HED formats. 
@@ -126,14 +126,14 @@ The most common types of BIDS tabular files are shown in the following table.
 (tabular-types-anchor)=
 | Ends with            | Time? | A row represents                                   |
 |----------------------|-------|----------------------------------------------------| 
-| `_events.tsv`        | Yes   | Markers on the timeline of another file.           | 
-| `_participants.tsv`  | No    | Metadata about one dataset subject.                |
-| `_scans.tsv`         | No    | Metadata about one dataset recording.              | 
-| `_beh.tsv`           | No    | A measurement not associated with an `onset`. |  
-| `_samples.tsv `      | No    | Properties of a particular sample (e.g., tissue).  |
-| `phenotype/xxx_.tsv` | No    | A measurement from a particular participant.       |  
-
-HED treats tabular files such as (e.g., `_events.tsv` files) whose first column has 
+| `events.tsv`        | Yes   | Markers on the timeline of another file.           | 
+| `participants.tsv`  | No    | Metadata about one dataset subject.                |
+| `scans.tsv`         | No    | Metadata about one dataset recording.              | 
+| `beh.tsv`           | No    | A measurement not associated with an `onset`. |  
+| `samples.tsv `      | No    | Properties of a particular sample (e.g., tissue).  |
+| `phenotype/xxx.tsv` | No    | A measurement from a particular participant.       |  
+
+HED treats tabular files such as (e.g., `events.tsv` files) whose first column has 
 the name `onset` as expressing markers on a timeline.
 These timeline files allow `Onset`, `Inset`, and `Offset` tags in their
 annotations and receive additional [**file-level processing**](./03_HED_formats.md#32104-file-level-processing) to assure that these tags are properly
@@ -146,7 +146,7 @@ for additional information.
 
 The following shows an excerpt from a BIDS event file:
 
-````{admonition} **Example:** Excerpt from a BIDS _events.tsv file.
+````{admonition} **Example:** Excerpt from a BIDS events.tsv file.
 
 ```
 onset  duration  trial_type  response_time  HED
@@ -255,7 +255,7 @@ It is possible to include library schema in the HED version specification of the
 The version specification indicates that tags from the `score` library must be prefixed with `sc:` 
 namespace identifier in dataset HED annotations.
 
-The prefix notation (such as the `sc:` prefix for the `score` library in the previous example is required when more than one schema is used in the annotation.
+The prefix notation (such as the `sc:` prefix for the `score` library in the previous example) is required when more than one schema is used in the annotation.
 However, namespace prefixes can be used with the standard schema as well as library schemas
 as illustrated by the following example.
 

docs/source/07_Library_schemas.md

@@ -403,7 +403,7 @@ As part of the HED annotation process, users must associate one or more
 HED schemas with their datasets.
 Since it would be impossible to avoid naming conflicts across schema libraries built in parallel by different user communities, 
 HED supports schema library namespaces to facilitate the use of multiple schemas in
-annotating a datasets..
+annotating a datasets.
 
 If multiple schemas are used, users must define a local namespace for
 each additional schema and prefix the tags from each of these

docs/source/Appendix_A.md

@@ -570,7 +570,7 @@ HED library="testlib" version="1.0.2"
 
 The `library` and `version` values are used to form the official file name `HED_testlib_1.0.2.mediawiki`.
 The file is found in [**library_schemas/testlib/hedwiki**](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/testlib/hedwiki)
-directory of the [**hed-schemas**](https://github.com/hed-standard/hedschemas) GitHub repository.
+directory of the [**hed-schemas**](https://github.com/hed-standard/hed-schemas) GitHub repository.
 
 A warning is generated when unknown header-line attributes are translated as attributes of the `HED` line
 during `.mediawiki` file validation.

docs/source/Appendix_B.md

@@ -440,7 +440,7 @@ schema attributes, properties and epilogue) are not in the correct order and hen
 **a.**  Delimiters used in the wiki are invalid.    
 **b.**  Schema line content after node name is not enclosed with `<nowiki></nowiki>` delimiters.  
 **c.**  A line has unmatched or multiple `<nowiki></nowiki>`, `[ ]`, or `{ }` delimiters.  
-**d.**  Attributes section of a node is malformed(eg hanging `=` character).
+**d.**  Attributes section of a node is malformed(e.g., hanging `=` character).
 
 #### WIKI_LINE_START_INVALID